SMTL ID : 5ij1.1

SrpA adhesin in complex with sialyllactose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

1 x BGC- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

BGC-GAL-SIA.1: 8 residues within 4Å: Chain A: T.45, F.46, R.94, Q.96, F.97, T.98, R.99, Y.120 6 PLIP interactions: 6 interactions with chain A Water bridges: A:T.98, A:T.98 Hydrogen bonds: A:Q.96, A:Q.96, A:T.98, A:R.99, A:R.99

7 x CA: CALCIUM ION(Non-covalent)

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.6, H2O.15, H2O.18 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:T.7, B:D.33, B:D.34, B:D.105 CA.8: 2 residues within 4Å: Chain B: N.61 Ligands: ACT.12 No protein-ligand interaction detected (PLIP) CA.9: 4 residues within 4Å: Chain B: T.124, Y.127, N.128, 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.18, H2O.22 CA.10: 1 residues within 4Å: Chain B: D.125 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.125, H2O.17, H2O.21, H2O.23, H2O.25

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

ACT.5: 4 residues within 4Å: Chain A: T.169, V.170 Chain B: R.167, T.169 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.11: 4 residues within 4Å: Chain A: R.167, T.169 Chain B: T.169, V.170 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:R.167, B:K.148 Salt bridges: A:R.167 Hydrogen bonds: B:V.170 ACT.12: 6 residues within 4Å: Chain B: N.61, V.64, P.65, G.66, N.67 Ligands: CA.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.64 Hydrogen bonds: B:N.61 Water bridges: B:N.67

Links

RCSB   PDBe   PDBe-KB   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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