SMTL ID : 3qv4.1

Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with dipeptide L-ALA D-GLU at 2.7 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

1 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-NAG-NAG.1: 9 residues within 4Å: Chain B: H.37, T.38, A.39, H.60, Y.71, N.110, M.112, L.153, S.154 No protein-ligand interaction detected (PLIP)

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: E.77, R.114, P.117, R.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.114, A:R.119 Water bridges: A:R.114 GOL.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.4: 4 residues within 4Å: Chain A: S.139, N.140 Chain D: W.98, I.101 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.139 GOL.5: 3 residues within 4Å: Chain A: T.38, V.56, Y.59 No protein-ligand interaction detected (PLIP) GOL.11: 10 residues within 4Å: Chain C: P.151, T.152, L.153 Chain D: H.37, T.38, A.39, Y.71, H.93, H.146 Ligands: SRT.10 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:T.38, D:Y.71, D:H.93, C:P.151, C:L.153

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 1 residues within 4Å: Chain A: A.129 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 6 residues within 4Å: Chain B: D.2, A.5, C.6, L.134 Chain D: R.31, R.138 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Water bridges: B:D.2, B:D.2 Hydrogen bonds: D:R.31

1 x ALA: ALANINE(Non-covalent)

ALA.8: 7 residues within 4Å: Chain A: R.31, N.140, E.142 Chain C: G.65, W.66 Chain D: T.97 Ligands: DGL.9 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:N.140, D:T.97, D:T.97 Water bridges: A:R.170, A:R.170

1 x DGL: D-GLUTAMIC ACID(Non-covalent)

DGL.9: 7 residues within 4Å: Chain C: W.66, R.85, G.91, A.92 Chain D: P.96, Q.150 Ligands: ALA.8 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:A.92 Hydrogen bonds: C:W.66, C:N.99, D:Q.150 Salt bridges: C:R.85, C:K.90

1 x SRT: S,R MESO-TARTARIC ACID(Non-covalent)

SRT.10: 11 residues within 4Å: Chain C: H.37, A.39, T.152, L.153, S.154 Chain D: H.37, A.39, T.152, L.153, S.154 Ligands: GOL.11 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:L.153, C:S.154, D:L.153 Salt bridges: C:H.37, D:H.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shukla, P.K. et al., Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with dipeptide L-ALA D-GLU at 2.7 A resolution. To be Published

Release Date

2011-03-30

Peptides

Peptidoglycan recognition protein 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Peptidoglycan recognition protein 1

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