SMTL ID : 2aph.3 (2 other biounits)

Crystal structure of human PGRP-IalphaC in complex with muramyl pentapeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ALA- GMA- LYS- DAL- DAL- NH2: muramyl pentapeptide(Non-covalent)

ALA-GMA-LYS-DAL-DAL-NH2.1: 12 residues within 4Å: Chain A: R.59, N.60, F.61, S.87, H.88, T.89, Y.90, G.91, N.93, V.144, I.146 Ligands: AMU.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.61, A:F.61, A:Y.90 Hydrogen bonds: A:R.59, A:H.88, A:Y.90, A:G.91, A:N.93 Water bridges: A:Y.90, A:Y.90 ALA-GMA-LYS-DAL-DAL-NH2.4: 14 residues within 4Å: Chain B: H.55, R.59, N.60, F.61, S.87, H.88, T.89, Y.90, G.91, N.93, H.140, V.144, I.146 Ligands: AMU.6 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.61, B:F.61, B:F.61, B:Y.90 Hydrogen bonds: B:R.59, B:N.60, B:H.88, B:Y.90, B:G.91, B:N.93 Water bridges: B:N.60, B:S.87, B:Y.90, B:Y.90

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: P.133, H.162 Chain B: P.133, H.162 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.133, B:P.133 Salt bridges: A:H.162, B:H.162 SO4.5: 9 residues within 4Å: Chain A: S.158, T.159, W.160, F.163, H.165 Chain B: S.158, W.160, F.163, H.165 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:H.165, A:H.165 Hydrogen bonds: A:W.160, A:F.163

2 x AMU: N-acetyl-beta-muramic acid(Non-covalent)

AMU.3: 11 residues within 4Å: Chain A: I.31, H.32, T.33, A.34, F.54, H.55, Y.66, H.140, I.146, S.148 Ligands: ALA-GMA-LYS-DAL-DAL-NH2.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.146 Hydrogen bonds: A:T.33, A:T.33, A:Y.66 Water bridges: A:R.59, A:L.147 AMU.6: 12 residues within 4Å: Chain B: I.31, H.32, T.33, A.34, I.51, F.54, H.55, Y.66, H.140, I.146, S.148 Ligands: ALA-GMA-LYS-DAL-DAL-NH2.4 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.51, B:I.146 Hydrogen bonds: B:T.33, B:T.33, B:Y.66 Water bridges: B:L.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guan, R. et al., Crystal structure of human peptidoglycan recognition protein I alpha bound to a muramyl pentapeptide from Gram-positive bacteria. Protein Sci. (2006)

Release Date

2006-06-27

Peptides

Peptidoglycan recognition protein I-alpha: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Peptidoglycan recognition protein I-alpha

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