SMTL ID : 5eq3.2 (1 other biounit)

Crystal structure of the SrpA adhesin from Streptococcus sanguinis with a sialyl galactose disaccharide bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

2 x MBG- NGC: N-glycolyl-alpha-neuraminic acid-(2-3)-methyl beta-D-galactopyranoside(Non-covalent)

MBG-NGC.1: 8 residues within 4Å: Chain A: F.46, R.94, A.95, Q.96, F.97, T.98, R.99, Y.120 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.96, A:Q.96, A:Q.96, A:T.98, A:R.99, A:R.99, A:Y.120, A:Y.120 Water bridges: A:T.98 MBG-NGC.13: 8 residues within 4Å: Chain C: F.46, R.94, A.95, Q.96, F.97, T.98, R.99, Y.120 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Q.96, C:Q.96, C:Q.96, C:T.98, C:T.98, C:R.99, C:R.99, C:Y.120 Water bridges: C:T.98

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

CA.2: 2 residues within 4Å: Chain A: E.152 Chain B: E.152 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.152, B:E.152, H2O.1, H2O.3, H2O.10 CA.3: 5 residues within 4Å: Chain A: D.5, T.7, D.33, D.34, D.105 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.5, A:T.7, A:D.33, A:D.34, A:D.105 CA.4: 3 residues within 4Å: Chain A: T.124, Y.127, D.186 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.124, A:Y.127, A:D.186, H2O.1, H2O.4 CA.7: 5 residues within 4Å: Chain B: D.5, T.7, D.33, D.34, D.105 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.5, B:D.5, B:T.7, B:D.33, B:D.105 CA.8: 3 residues within 4Å: Chain B: T.124, Y.127, D.186 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Y.127, B:D.186, B:D.186, H2O.10, H2O.10 CA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.10: 1 residues within 4Å: Chain B: D.125 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.125, H2O.12, H2O.21, H2O.26 CA.14: 2 residues within 4Å: Chain C: E.152 Chain D: E.152 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: C:E.152, D:E.152, H2O.15, H2O.17, H2O.23 CA.15: 5 residues within 4Å: Chain C: D.5, T.7, D.33, D.34, D.105 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.5, C:T.7, C:D.33, C:D.34, C:D.105 CA.16: 3 residues within 4Å: Chain C: T.124, Y.127, D.186 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.124, C:Y.127, C:D.186, H2O.15, H2O.17 CA.19: 5 residues within 4Å: Chain D: D.5, T.7, D.33, D.34, D.105 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.5, D:D.5, D:T.7, D:D.33, D:D.105 CA.20: 3 residues within 4Å: Chain D: T.124, Y.127, D.186 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:Y.127, D:D.186, D:D.186, H2O.23, H2O.24 CA.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.22: 1 residues within 4Å: Chain D: D.125 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.125, H2O.8, H2O.13, H2O.25

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

ACT.5: 6 residues within 4Å: Chain A: K.148, T.169, V.170 Chain B: R.167, T.169 Ligands: ACT.12 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.170 Water bridges: A:K.148, A:K.148, A:V.170, B:R.167 Salt bridges: B:R.167 ACT.6: 3 residues within 4Å: Chain A: P.49, L.50, G.51 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.50, A:G.51 Water bridges: A:L.52, A:N.53 ACT.12: 5 residues within 4Å: Chain A: R.167, T.169 Chain B: T.169, V.170 Ligands: ACT.5 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:R.167, A:R.167 Salt bridges: A:R.167 Hydrogen bonds: B:V.170 ACT.17: 6 residues within 4Å: Chain C: K.148, T.169, V.170 Chain D: R.167, T.169 Ligands: ACT.24 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:V.170 Water bridges: C:K.148, C:K.148, C:V.170, D:R.167 Salt bridges: D:R.167 ACT.18: 3 residues within 4Å: Chain C: P.49, L.50, G.51 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.50, C:G.51 Water bridges: C:L.52, C:N.53 ACT.24: 5 residues within 4Å: Chain C: R.167, T.169 Chain D: T.169, V.170 Ligands: ACT.17 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Water bridges: C:R.167, C:R.167 Salt bridges: C:R.167 Hydrogen bonds: D:V.170

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

NA.11: 0 residues within 4Å: (No contacts) 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.61, B:N.67, B:P.73 NA.23: 0 residues within 4Å: (No contacts) 3 PLIP interactions: 3 interactions with chain D Water bridges: D:N.61, D:G.66, D:P.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bensing, B.A. et al., Structural Basis for Sialoglycan Binding by the Streptococcus sanguinis SrpA Adhesin. J.Biol.Chem. (2016)

Release Date

2016-01-27

Peptides

Platelet-binding glycoprotein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Platelet-binding glycoprotein

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