SMTL ID : 6ef9.1 (1 other biounit)

GspB Siglec domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

6 x NA: SODIUM ION(Non-functional Binders)

NA.1: 9 residues within 4Å: Chain A: E.7, P.9, D.33, N.34, S.35, D.96, N.100 Ligands: FMT.10, FMT.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.33, A:D.96, A:N.100 NA.2: 2 residues within 4Å: Chain A: N.12 Ligands: NA.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.12 NA.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.4: 4 residues within 4Å: Chain A: D.33, N.34, N.36, N.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.36 Water bridges: A:D.33, A:D.33 NA.5: 1 residues within 4Å: Chain A: S.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.24 Water bridges: A:S.24 NA.6: 1 residues within 4Å: Ligands: NA.2 No protein-ligand interaction detected (PLIP)

5 x FMT: FORMIC ACID(Non-functional Binders)

FMT.7: 5 residues within 4Å: Chain A: R.46, Y.49, S.50, Q.105 Ligands: FMT.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.46, A:R.46, A:Q.105 FMT.8: 4 residues within 4Å: Chain A: R.46, S.50, N.51 Ligands: FMT.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.51 FMT.9: 2 residues within 4Å: Chain A: S.50, Q.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.50, A:Q.52 FMT.10: 7 residues within 4Å: Chain A: E.7, D.33, S.35, D.96, A.98, N.100 Ligands: NA.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.35, A:D.96, A:N.100 Water bridges: A:A.98 FMT.11: 10 residues within 4Å: Chain A: T.6, E.7, R.8, P.9, V.10, T.32, D.33, N.34, S.35 Ligands: NA.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.34 Water bridges: A:R.8, A:R.8, A:T.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bensing, B.A. et al., Origins of glycan selectivity in streptococcal Siglec-like adhesins suggest mechanisms of receptor adaptation. Nat Commun (2022)

Release Date

2020-02-19

Peptides

Platelet binding protein GspB - Siglec domain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Platelet binding protein GspB - Siglec domain

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