SMTL ID : 5ij3.1

SrpA adhesin in complex with sialyl T antigen

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

1 x A2G- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G-GAL-SIA.1: 7 residues within 4Å: Chain A: F.43, R.91, Q.93, F.94, T.95, R.96, Y.117 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.93, A:Q.93, A:T.95, A:R.96, A:R.96 Water bridges: A:T.95

7 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 2 residues within 4Å: Chain A: E.149 Chain B: E.149 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.149, A:E.149, A:E.149, H2O.16, H2O.18 CA.3: 5 residues within 4Å: Chain A: D.2, T.4, D.30, D.31, D.102 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.2, A:T.4, A:D.30, A:D.31, A:D.102 CA.4: 4 residues within 4Å: Chain A: T.121, Y.124, D.183 Ligands: ACT.7 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:T.121, A:Y.124, A:D.183, H2O.4, ACT.7 CA.8: 5 residues within 4Å: Chain B: D.2, T.4, D.30, D.31, D.102 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.2, B:T.4, B:D.30, B:D.31, B:D.102 CA.9: 1 residues within 4Å: Ligands: ACT.13 4 PLIP interactions: 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: ACT.13, H2O.14, H2O.16, H2O.22 CA.10: 3 residues within 4Å: Chain B: T.121, Y.124, D.183 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.121, B:Y.124, B:D.183, H2O.17, H2O.17 CA.11: 1 residues within 4Å: Chain B: D.122 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.17, H2O.19, H2O.22, H2O.22, H2O.26

6 x ACT: ACETATE ION(Non-covalent)(Non-functional Binders)

ACT.5: 4 residues within 4Å: Chain A: T.166, V.167 Chain B: R.164, T.166 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.167 Water bridges: A:K.145, A:K.145, A:V.167, B:R.164 Salt bridges: B:R.164 ACT.6: 3 residues within 4Å: Chain A: P.46, L.47, G.48 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.47, A:G.48 Water bridges: A:L.49, A:N.50 ACT.7: 4 residues within 4Å: Chain A: T.121, T.182, D.183 Ligands: CA.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.121 ACT.12: 4 residues within 4Å: Chain A: R.164, T.166 Chain B: T.166, V.167 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:V.167 Water bridges: B:K.145, A:R.164 Salt bridges: A:R.164 ACT.13: 6 residues within 4Å: Chain B: N.58, V.61, P.62, G.63, N.64 Ligands: CA.9 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.61 Hydrogen bonds: B:N.58 ACT.14: 5 residues within 4Å: Chain B: D.57, N.58, P.70, L.71, R.72 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.71, B:R.72 Hydrogen bonds: B:N.58, B:R.72 Water bridges: B:S.55

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Loukachevitch, L.V. et al., Structures of the Streptococcus sanguinis SrpA Binding Region with Human Sialoglycans Suggest Features of the Physiological Ligand. Biochemistry (2016)

Release Date

2017-02-08

Peptides

Platelet-binding glycoprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Platelet-binding glycoprotein

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