6OYC | pdb_00006oyc

Glycosylation Associate Protein (Gap123) complex from Streptococcus agalactiae

PDB DOI: https://doi.org/10.2210/pdb6OYC/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Streptococcus agalactiae 2603V/R
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-05-14 Released: 2020-05-20
Deposition Author(s): zhang, H., Wu, H.
Funding Organization(s): National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.227 (Depositor), 0.227 (DCC)
R-Value Work:
0.181 (Depositor), 0.183 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Glycosylation Associate Protein (Gap123) complex from Streptococcus agalactiae

zhang, H., Zhu, F., Wu, H.

To be published.

Macromolecule Content

Total Structure Weight: 159.21 kDa
Atom Count: 11,323
Modeled Residue Count: 1,325
Deposited Residue Count: 1,363
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosylation Associate Protein 1	A	514	Streptococcus agalactiae 2603V/R	Mutation(s): 0 Gene Names: SAG1452
UniProt
Find proteins for Q8DYM4 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)) Explore Q8DYM4 Go to UniProtKB: Q8DYM4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DYM4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosylation Associate Protein 2	B	519	Streptococcus agalactiae 2603V/R	Mutation(s): 0 Gene Names: SAG1451
UniProt
Find proteins for Q8DYM5 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)) Explore Q8DYM5 Go to UniProtKB: Q8DYM5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DYM5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosylation Associate Protein 3	C	330	Streptococcus agalactiae 2603V/R	Mutation(s): 0 Gene Names: SAG1450
UniProt
Find proteins for Q8DYM6 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)) Explore Q8DYM6 Go to UniProtKB: Q8DYM6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DYM6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B]	J [auth A], K [auth A], P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C]