SMTL ID : 5eq2.1

Crystal Structure of the SrpA Adhesin from Streptococcus sanguinis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

CA.1: 2 residues within 4Å: Chain A: E.152 Chain B: E.152 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.152, A:E.152, H2O.4, H2O.12, H2O.13 CA.2: 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.3: 4 residues within 4Å: Chain A: T.124, Y.127, D.186 Ligands: ACT.6 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:Y.127, A:D.186, H2O.4, H2O.4, ACT.6 CA.8: 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:T.7, B:D.33, B:D.34, B:D.105 CA.9: 1 residues within 4Å: Ligands: ACT.13 No protein-ligand interaction detected (PLIP) CA.10: 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:T.124, B:Y.127, B:D.186, H2O.14, H2O.16 CA.11: 1 residues within 4Å: Chain B: D.125 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.14, H2O.17, H2O.18, H2O.20, H2O.20

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

ACT.4: 4 residues within 4Å: Chain A: T.169, V.170 Chain B: R.167, T.169 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.170 Water bridges: A:K.148, A:K.148, A:K.148, A:K.148, B:R.167 Salt bridges: B:R.167 ACT.5: 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.6: 4 residues within 4Å: Chain A: T.124, T.185, D.186 Ligands: CA.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.124 Water bridges: A:D.125, A:N.128 ACT.7: 2 residues within 4Å: Chain A: E.56, Y.57 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.57 Hydrogen bonds: A:Y.57 ACT.12: 4 residues within 4Å: Chain A: R.167, T.169 Chain B: T.169, V.170 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:V.170 Water bridges: B:K.148, A:R.167 Salt bridges: A:R.167 ACT.13: 6 residues within 4Å: Chain B: N.61, V.64, P.65, G.66, N.67 Ligands: CA.9 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.64 Hydrogen bonds: B:N.61 Water bridges: B:N.61 ACT.14: 5 residues within 4Å: Chain B: D.60, N.61, P.73, L.74, R.75 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.74 Hydrogen bonds: B:N.61, B:R.75 Water bridges: B:S.58 ACT.15: 3 residues within 4Å: Chain B: E.56, Y.57, E.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.57, B:E.59

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Platelet-binding glycoprotein

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