Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

LJ
Luca Jovine
Fri, Dec 4, 2020 8:20 AM

Yes Tristan, that would be even better - also because such an Ag1, Ag2,… system could conveniently fall back on a single-character chain A, when generating legacy PDB format files from the mmCIF ones.
Exactly for the reason that you pointed out, personally I do not understand the logic of assigning a different chain ID to covalently attached glycans (or any other covalent post-translational modification, for that matter). Aren't residue IDs enough to make it clear that such residues are not amino acids?
-Luca

On 4 Dec 2020, at 09:06, Tristan Croll tic20@cam.ac.uk wrote:

To go one step further: in large, heavily glycosylated multi-chain complexes the assignment of a random new chain ID to each glycan will lead to headaches for people building visualisations using existing viewers, because it loses the easy name-based association of glycan to parent protein chain. A suggestion: why not take full advantage of the mmCIF capability for multi-character chain IDs, and name them by appending characters to the parent chain ID? Using chain A as an example, perhaps the glycans could become Ag1, Ag2, etc.?

On 4 Dec 2020, at 07:48, Luca Jovine luca.jovine@ki.se wrote:

CC: pdb-l

Dear Zhijie and Robbie,

I agree with both of you that the new carbohydrate chain assignment convention that has been recently adopted by PDB introduces confusion, not just for PDB-REDO but also - and especially - for end users.

Could we kindly ask PDB to improve consistency by either assigning a separate chain to all covalently attached carbohydrates (regardless of whether one or more residues have been traced), or reverting to the old system (where N-/O-glycans inherited the same chain ID of the protein to which they are attached)? The current hybrid solution hardly seems optimal...

Best regards,

Luca

On 3 Dec 2020, at 20:17, Robbie Joosten robbie_joosten@HOTMAIL.COM wrote:

Dear Zhijie,

In generally I like the treatment of carbohydrates now as branched polymers. I didn't realise there was an exception. It makes sense for unlinked carbohydrate ligands, but not for N- or O-glycosylation sites as these might change during model building or, in my case, carbohydrate rebuilding in PDB-REDO powered by Coot. Thanks for pointing this out.

Cheers,
Robbie

-----Original Message-----
From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK On Behalf Of Zhijie Li
Sent: Thursday, December 3, 2020 19:52
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the
PDB -- N-glycans are now separate chains if more than one residue

Hi all,

I was confused when I saw mysterious new glycan chains emerging during
PDB deposition and spent quite some time trying to find out what was
wrong with my coordinates.  Then it occurred to me that a lot of recent
structures also had tens of N-glycan chains.  Finally I realized that this
phenomenon is a consequence of this PDB policy announced here in July.

For future depositors who might also get puzzled, let's put it in a short
sentence:  O- and N-glycans are now separate chains if it they contain more
than one residue; single residues remain with the protein chain.

https://urldefense.com/v3/https://eur01.safelinks.protection.outlook.com/?url=https3A2F2Fwww.wwpdb.org2Fdocumentation2Fcarbohydrate-remediation&data=047C017Cluca.jovine40ki.se7Ca3fed8eed9d94a481d6808d8982b731f7Cbff7eef1cf4b4f32be3da1dda043c05d7C07C17C6374266596662446137CUnknown7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn03D7C1000&sdata=BqPiPeexG0nLhUmaih2Bq8ppjkX2F2BbLP4SoBGL4u52Fw*3D&reserved=0;JSUlJSUlJSUlJSUlJSUlJSUlJSUl!!Mih3wA!X8HRMicNnFsCt1DuLX3uh9_3Xqlz8Q0re3P5a8sdHzzmrLo52AcQQ003cxlTliI$

"Oligosaccharide molecules are classified as a new entity type, branched,
assigned a unique chain ID (_atom_site.auth_asym_id) and a new mmCIF
category introduced to define the type of branching
(_pdbx_entity_branch.type) . "

I found the differential treatment of single-residue glycans and multi-residue
glycans not only bit lack of aesthetics but also misleading.  When a structure
contains both NAG-NAG... and single NAG on N-glycosylation sites, it might
be because of lack of density for building more residues, or because that
some of the glycosylation sites are now indeed single NAGs (endoH etc.)
while some others are not cleaved due to accessibility issues.    Leaving NAGs
on the protein chain while assigning NAG-NAG... to a new chain, feels like
suggesting something about their true oligomeric state.

For example, for cryoEM structures, when one only builds a single NAG at a
site does not necessarily mean that the protein was treated by endoH. In
fact all sites are extended to at least tri-Man in most cases. Then why
keeping some sites associated with the protein chain while others kicked
out?

Zhijie


From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK on behalf of John
Berrisford jmb@EBI.AC.UK
Sent: Thursday, July 9, 2020 4:39 AM
To: CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB

Dear CCP4BB

PDB data will shortly incorporate a new data representation for
carbohydrates in PDB entries and reference data that improves the
Findability and Interoperability of these molecules in macromolecular
structures. In order to remediate and improve the representation of
carbohydrates across the archive, the wwPDB has:

*standardized Chemical Component Dictionary nomenclature
following IUPAC-IUBMB recommendations
*provided uniform representation for oligosaccharides
*adopted Glycoscience-community commonly used linear descriptors
using community tools
*annotated glycosylation sites in PDB structures

Starting July 29, 2020, users will be able to access the improved data via FTP
or wwPDB partner websites. Detailed information about this project is
available at the wwPDB website
<https://urldefense.com/v3/https://eur01.safelinks.protection.outlook.com/?url=https3A2F2Fwww.wwpdb.org2Fdocumentation2Fcarbohydrate-remediation&data=047C017Cluca.jovine40ki.se7Ca3fed8eed9d94a481d6808d8982b731f7Cbff7eef1cf4b4f32be3da1dda043c05d7C07C17C6374266596662446137CUnknown7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn03D7C1000&sdata=BqPiPeexG0nLhUmaih2Bq8ppjkX2F2BbLP4SoBGL4u52Fw*3D&reserved=0;JSUlJSUlJSUlJSUlJSUlJSUlJSUl!!Mih3wA!X8HRMicNnFsCt1DuLX3uh9_3Xqlz8Q0re3P5a8sdHzzmrLo52AcQQ003cxlTliI$ > ; lists
of impacted entries and chemical components will be published on this page
after data release.

The wwPDB has created a new ‘branched’ entity representation for
polysaccharides, describing all the individual monosaccharide components of
these in the PDB entry. As part of this process, we have standardized atom
nomenclature of >1,000 monosaccharides in the Chemical Component
Dictionary (CCD) and applied a branched entity representation to
oligosaccharides for >8000 PDB entries. To guarantee unambiguous chemical
description of oligosaccharides in the affected PDB entries, an explicit
description of covalent linkage information between their monosaccharide
units is included. In addition, wwPDB validation reports provide consistent
representation for these oligosaccharides and include 2D representations
based on the Symbol Nomenclature for Glycans (SNFG).

To support the remediation of carbohydrate representation, software tools
providing linear descriptors were developed in collaboration with the
glycoscience community to enable easy translation of PDB data to other
representations commonly used by glycobiologists. These include Condense
IUPAC from GMML <https://urldefense.com/v3/https://eur01.safelinks.protection.outlook.com/?url=https3A2F2Fgithub.com2FGLYCAM-Web2Fgmml&data=047C017Cluca.jovine40ki.se7Ca3fed8eed9d94a481d6808d8982b731f7Cbff7eef1cf4b4f32be3da1dda043c05d7C07C17C6374266596662545697CUnknown7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn03D7C1000&sdata=ZfvfU2FBudQysETQjHkvR3NPuF8AWyGaNJ2BirouL23BA3D&reserved=0;JSUlJSUlJSUlJSUlJSUlJSUlJSU!!Mih3wA!X8HRMicNnFsCt1DuLX3uh9_3Xqlz8Q0re3P5a8sdHzzmrLo52AcQQ003qgzx6R8$ >  at University
of Georgia, WURCS <https://urldefense.com/v3/https://eur01.safelinks.protection.outlook.com/?url=https3A2F2Fgitlab.com2Fglyconavi2Fpdb2glycan&data=047C017Cluca.jovine40ki.se7Ca3fed8eed9d94a481d6808d8982b731f7Cbff7eef1cf4b4f32be3da1dda043c05d7C07C17C6374266596662545697CUnknown7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn03D7C1000&sdata=8FaXeDf8Hk2BUB1BVsGRm4KL6ALdDEtS1HGbik28T12B83D&reserved=0;JSUlJSUlJSUlJSUlJSUlJSUlJSU!!Mih3wA!X8HRMicNnFsCt1DuLX3uh9_3Xqlz8Q0re3P5a8sdHzzmrLo52AcQQ003Q9tvdDE$ >  from
PDB2Glycan at The Noguchi Institute, Japan, and LINUCS
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Germany.

Furthermore, to ensure continued Findability of 118 common
oligosaccharides (e.g., sucrose, Lewis Y antigen), we have expanded the
Biologically Interesting molecule Reference Dictionary (BIRD
<https://urldefense.com/v3/https://eur01.safelinks.protection.outlook.com/?url=https3A2F2Fwww.wwpdb.org2Fdata2Fbird&data=047C017Cluca.jovine40ki.se7Ca3fed8eed9d94a481d6808d8982b731f7Cbff7eef1cf4b4f32be3da1dda043c05d7C07C17C6374266596662545697CUnknown7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn03D7C1000&sdata=1pqguhV4s5Ajh1ctx0CDE0zNSefDGK8qwQl9lky2BSPs*3D&reserved=0;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!X8HRMicNnFsCt1DuLX3uh9_3Xqlz8Q0re3P5a8sdHzzmrLo52AcQQ003-nkhsnc$ > ) that contains the covalent linkage
information and common synonyms for such molecules.

wwPDB has also used this opportunity to improve the organization of
chemical synonyms in the CCD by introducing a new
_pdbx_chem_comp_synonyms data category. This will enable more
comprehensive capture of alternative names for small molecules in the PDB.
To minimize disruption to users, the legacy data item,
_chem_comp.pdbx_synonyms, will be retained for a transition period
through 2021.

The carbohydrate remediation project is a wwPDB collaborative project that
is carried out principally by RCSB PDB <https://urldefense.com/v3/https://eur01.safelinks.protection.outlook.com/?url=https3A2F2Fwww.rcsb.org2F&data=047C017Cluca.jovine40ki.se7Ca3fed8eed9d94a481d6808d8982b731f7Cbff7eef1cf4b4f32be3da1dda043c05d7C07C07C6374266596662545697CUnknown7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn03D7C1000&sdata=Y22BaEG2JioqaVYp8Q0Mpq0f8yzraA5Jnehsi0kjhsaE3D&reserved=0;JSUlJSUlJSUlJSUlJSUlJSUl!!Mih3wA!X8HRMicNnFsCt1DuLX3uh9_3Xqlz8Q0re3P5a8sdHzzmrLo52AcQQ003Ir-C3iY$ >  at Rutgers,
The State University of New Jersey and is funded by NIGMS grant U01
CA221216 in collaboration with Complex Carbohydrate Research Center
<https://urldefense.com/v3/https://eur01.safelinks.protection.outlook.com/?url=https3A2F2Fwww.ccrc.uga.edu2F&data=047C017Cluca.jovine40ki.se7Ca3fed8eed9d94a481d6808d8982b731f7Cbff7eef1cf4b4f32be3da1dda043c05d7C07C07C6374266596662545697CUnknown7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn03D7C1000&sdata=K9KewAawbZOOuPMgKdNDk78U2BkjNQD1YPqiJyxwkhZU3D&reserved=0;JSUlJSUlJSUlJSUlJSUlJSUl!!Mih3wA!X8HRMicNnFsCt1DuLX3uh9_3Xqlz8Q0re3P5a8sdHzzmrLo52AcQQ003N2jKXgY$ >  at the University of Georgia.

If you have any comments or queries regarding the changes to carbohydrate
representation, please visit the wwPDB website
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contact us at deposit-help@mail.wwpdb.org <mailto:deposit-
help@mail.wwpdb.org> .

Regards

John

--

John Berrisford

PDBe

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

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Yes Tristan, that would be even better - also because such an Ag1, Ag2,… system could conveniently fall back on a single-character chain A, when generating legacy PDB format files from the mmCIF ones. Exactly for the reason that you pointed out, personally I do not understand the logic of assigning a different chain ID to covalently attached glycans (or any other covalent post-translational modification, for that matter). Aren't residue IDs enough to make it clear that such residues are not amino acids? -Luca > On 4 Dec 2020, at 09:06, Tristan Croll <tic20@cam.ac.uk> wrote: > > To go one step further: in large, heavily glycosylated multi-chain complexes the assignment of a random new chain ID to each glycan will lead to headaches for people building visualisations using existing viewers, because it loses the easy name-based association of glycan to parent protein chain. A suggestion: why not take full advantage of the mmCIF capability for multi-character chain IDs, and name them by appending characters to the parent chain ID? Using chain A as an example, perhaps the glycans could become Ag1, Ag2, etc.? > >> On 4 Dec 2020, at 07:48, Luca Jovine <luca.jovine@ki.se> wrote: >> >> CC: pdb-l >> >> Dear Zhijie and Robbie, >> >> I agree with both of you that the new carbohydrate chain assignment convention that has been recently adopted by PDB introduces confusion, not just for PDB-REDO but also - and especially - for end users. >> >> Could we kindly ask PDB to improve consistency by either assigning a separate chain to all covalently attached carbohydrates (regardless of whether one or more residues have been traced), or reverting to the old system (where N-/O-glycans inherited the same chain ID of the protein to which they are attached)? The current hybrid solution hardly seems optimal... >> >> Best regards, >> >> Luca >> >>> On 3 Dec 2020, at 20:17, Robbie Joosten <robbie_joosten@HOTMAIL.COM> wrote: >>> >>> Dear Zhijie, >>> >>> In generally I like the treatment of carbohydrates now as branched polymers. I didn't realise there was an exception. It makes sense for unlinked carbohydrate ligands, but not for N- or O-glycosylation sites as these might change during model building or, in my case, carbohydrate rebuilding in PDB-REDO powered by Coot. Thanks for pointing this out. >>> >>> Cheers, >>> Robbie >>> >>>> -----Original Message----- >>>> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Zhijie Li >>>> Sent: Thursday, December 3, 2020 19:52 >>>> To: CCP4BB@JISCMAIL.AC.UK >>>> Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the >>>> PDB -- N-glycans are now separate chains if more than one residue >>>> >>>> Hi all, >>>> >>>> I was confused when I saw mysterious new glycan chains emerging during >>>> PDB deposition and spent quite some time trying to find out what was >>>> wrong with my coordinates. Then it occurred to me that a lot of recent >>>> structures also had tens of N-glycan chains. Finally I realized that this >>>> phenomenon is a consequence of this PDB policy announced here in July. >>>> >>>> >>>> For future depositors who might also get puzzled, let's put it in a short >>>> sentence: O- and N-glycans are now separate chains if it they contain more >>>> than one residue; single residues remain with the protein chain. >>>> >>>> >>>> https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.wwpdb.org*2Fdocumentation*2Fcarbohydrate-remediation&amp;data=04*7C01*7Cluca.jovine*40ki.se*7Ca3fed8eed9d94a481d6808d8982b731f*7Cbff7eef1cf4b4f32be3da1dda043c05d*7C0*7C1*7C637426659666244613*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&amp;sdata=BqPiPeexG0nLhUmaih2Bq8ppjkX*2F*2BbLP4SoBGL4u5*2Fw*3D&amp;reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUl!!Mih3wA!X8HRMicNnFsCt1DuLX3uh9_3Xqlz8Q0re3P5a8sdHzzmrLo52AcQQ003cxlTliI$ >>>> >>>> "Oligosaccharide molecules are classified as a new entity type, branched, >>>> assigned a unique chain ID (_atom_site.auth_asym_id) and a new mmCIF >>>> category introduced to define the type of branching >>>> (_pdbx_entity_branch.type) . " >>>> >>>> >>>> >>>> >>>> >>>> I found the differential treatment of single-residue glycans and multi-residue >>>> glycans not only bit lack of aesthetics but also misleading. When a structure >>>> contains both NAG-NAG... and single NAG on N-glycosylation sites, it might >>>> be because of lack of density for building more residues, or because that >>>> some of the glycosylation sites are now indeed single NAGs (endoH etc.) >>>> while some others are not cleaved due to accessibility issues. Leaving NAGs >>>> on the protein chain while assigning NAG-NAG... to a new chain, feels like >>>> suggesting something about their true oligomeric state. >>>> >>>> >>>> For example, for cryoEM structures, when one only builds a single NAG at a >>>> site does not necessarily mean that the protein was treated by endoH. In >>>> fact all sites are extended to at least tri-Man in most cases. Then why >>>> keeping some sites associated with the protein chain while others kicked >>>> out? >>>> >>>> Zhijie >>>> >>>> >>>> >>>> ________________________________ >>>> >>>> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of John >>>> Berrisford <jmb@EBI.AC.UK> >>>> Sent: Thursday, July 9, 2020 4:39 AM >>>> To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> >>>> Subject: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB >>>> >>>> >>>> Dear CCP4BB >>>> >>>> PDB data will shortly incorporate a new data representation for >>>> carbohydrates in PDB entries and reference data that improves the >>>> Findability and Interoperability of these molecules in macromolecular >>>> structures. In order to remediate and improve the representation of >>>> carbohydrates across the archive, the wwPDB has: >>>> >>>> *standardized Chemical Component Dictionary nomenclature >>>> following IUPAC-IUBMB recommendations >>>> *provided uniform representation for oligosaccharides >>>> *adopted Glycoscience-community commonly used linear descriptors >>>> using community tools >>>> *annotated glycosylation sites in PDB structures >>>> >>>> Starting July 29, 2020, users will be able to access the improved data via FTP >>>> or wwPDB partner websites. Detailed information about this project is >>>> available at the wwPDB website >>>> <https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.wwpdb.org*2Fdocumentation*2Fcarbohydrate-remediation&amp;data=04*7C01*7Cluca.jovine*40ki.se*7Ca3fed8eed9d94a481d6808d8982b731f*7Cbff7eef1cf4b4f32be3da1dda043c05d*7C0*7C1*7C637426659666244613*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&amp;sdata=BqPiPeexG0nLhUmaih2Bq8ppjkX*2F*2BbLP4SoBGL4u5*2Fw*3D&amp;reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUl!!Mih3wA!X8HRMicNnFsCt1DuLX3uh9_3Xqlz8Q0re3P5a8sdHzzmrLo52AcQQ003cxlTliI$ > ; lists >>>> of impacted entries and chemical components will be published on this page >>>> after data release. >>>> >>>> The wwPDB has created a new ‘branched’ entity representation for >>>> polysaccharides, describing all the individual monosaccharide components of >>>> these in the PDB entry. As part of this process, we have standardized atom >>>> nomenclature of >1,000 monosaccharides in the Chemical Component >>>> Dictionary (CCD) and applied a branched entity representation to >>>> oligosaccharides for >8000 PDB entries. To guarantee unambiguous chemical >>>> description of oligosaccharides in the affected PDB entries, an explicit >>>> description of covalent linkage information between their monosaccharide >>>> units is included. In addition, wwPDB validation reports provide consistent >>>> representation for these oligosaccharides and include 2D representations >>>> based on the Symbol Nomenclature for Glycans (SNFG). >>>> >>>> To support the remediation of carbohydrate representation, software tools >>>> providing linear descriptors were developed in collaboration with the >>>> glycoscience community to enable easy translation of PDB data to other >>>> representations commonly used by glycobiologists. These include Condense >>>> IUPAC from GMML <https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fgithub.com*2FGLYCAM-Web*2Fgmml&amp;data=04*7C01*7Cluca.jovine*40ki.se*7Ca3fed8eed9d94a481d6808d8982b731f*7Cbff7eef1cf4b4f32be3da1dda043c05d*7C0*7C1*7C637426659666254569*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&amp;sdata=ZfvfU*2FBudQysETQjHkvR3NPuF8AWyGaNJ*2BirouL23BA*3D&amp;reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSU!!Mih3wA!X8HRMicNnFsCt1DuLX3uh9_3Xqlz8Q0re3P5a8sdHzzmrLo52AcQQ003qgzx6R8$ > at University >>>> of Georgia, WURCS <https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fgitlab.com*2Fglyconavi*2Fpdb2glycan&amp;data=04*7C01*7Cluca.jovine*40ki.se*7Ca3fed8eed9d94a481d6808d8982b731f*7Cbff7eef1cf4b4f32be3da1dda043c05d*7C0*7C1*7C637426659666254569*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&amp;sdata=8FaXeDf8Hk*2BUB1BVsGRm4KL6ALdDEtS1HGbik28T1*2B8*3D&amp;reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSU!!Mih3wA!X8HRMicNnFsCt1DuLX3uh9_3Xqlz8Q0re3P5a8sdHzzmrLo52AcQQ003Q9tvdDE$ > from >>>> PDB2Glycan at The Noguchi Institute, Japan, and LINUCS >>>> <https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=http*3A*2F*2Fwww.glycosciences.de*2Ftools*2Fpdb2linucs*2F&amp;data=04*7C01*7Cluca.jovine*40ki.se*7Ca3fed8eed9d94a481d6808d8982b731f*7Cbff7eef1cf4b4f32be3da1dda043c05d*7C0*7C1*7C637426659666254569*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&amp;sdata=qGJLV*2FzVgdyGcUQNDKOYIlPiyKn6z9P7E5j7G8tatRk*3D&amp;reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSU!!Mih3wA!X8HRMicNnFsCt1DuLX3uh9_3Xqlz8Q0re3P5a8sdHzzmrLo52AcQQ003gRpwnOg$ > from pdb-care at >>>> Germany. >>>> >>>> Furthermore, to ensure continued Findability of 118 common >>>> oligosaccharides (e.g., sucrose, Lewis Y antigen), we have expanded the >>>> Biologically Interesting molecule Reference Dictionary (BIRD >>>> <https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.wwpdb.org*2Fdata*2Fbird&amp;data=04*7C01*7Cluca.jovine*40ki.se*7Ca3fed8eed9d94a481d6808d8982b731f*7Cbff7eef1cf4b4f32be3da1dda043c05d*7C0*7C1*7C637426659666254569*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&amp;sdata=1pqguhV4s5Ajh1ctx0CDE0zNSefDGK8qwQl9lky*2BSPs*3D&amp;reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!X8HRMicNnFsCt1DuLX3uh9_3Xqlz8Q0re3P5a8sdHzzmrLo52AcQQ003-nkhsnc$ > ) that contains the covalent linkage >>>> information and common synonyms for such molecules. >>>> >>>> wwPDB has also used this opportunity to improve the organization of >>>> chemical synonyms in the CCD by introducing a new >>>> _pdbx_chem_comp_synonyms data category. This will enable more >>>> comprehensive capture of alternative names for small molecules in the PDB. >>>> To minimize disruption to users, the legacy data item, >>>> _chem_comp.pdbx_synonyms, will be retained for a transition period >>>> through 2021. >>>> >>>> The carbohydrate remediation project is a wwPDB collaborative project that >>>> is carried out principally by RCSB PDB <https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.rcsb.org*2F&amp;data=04*7C01*7Cluca.jovine*40ki.se*7Ca3fed8eed9d94a481d6808d8982b731f*7Cbff7eef1cf4b4f32be3da1dda043c05d*7C0*7C0*7C637426659666254569*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&amp;sdata=Y2*2BaEG2JioqaVYp8Q0Mpq0f8yzraA5Jnehsi0kjhsaE*3D&amp;reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUl!!Mih3wA!X8HRMicNnFsCt1DuLX3uh9_3Xqlz8Q0re3P5a8sdHzzmrLo52AcQQ003Ir-C3iY$ > at Rutgers, >>>> The State University of New Jersey and is funded by NIGMS grant U01 >>>> CA221216 in collaboration with Complex Carbohydrate Research Center >>>> <https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fwww.ccrc.uga.edu*2F&amp;data=04*7C01*7Cluca.jovine*40ki.se*7Ca3fed8eed9d94a481d6808d8982b731f*7Cbff7eef1cf4b4f32be3da1dda043c05d*7C0*7C0*7C637426659666254569*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&amp;sdata=K9KewAawbZOOuPMgKdNDk78U*2BkjNQD1YPqiJyxwkhZU*3D&amp;reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUl!!Mih3wA!X8HRMicNnFsCt1DuLX3uh9_3Xqlz8Q0re3P5a8sdHzzmrLo52AcQQ003N2jKXgY$ > at the University of Georgia. >>>> >>>> If you have any comments or queries regarding the changes to carbohydrate >>>> representation, please visit the wwPDB website >>>> 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