SMTL ID : 4ben.4 (3 other biounits)

R39-imipenem Acyl-enzyme crystal structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x IM2: (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid(Covalent)

IM2.1: 12 residues within 4Å: Chain A: A.48, S.49, S.298, N.300, G.348, L.349, T.393, K.410, T.411, G.412, T.413, M.414 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.349 Hydrogen bonds: A:S.49, A:S.298, A:S.298, A:S.298, A:N.300, A:T.411, A:T.413 Salt bridges: A:K.410

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.188, H.247, E.251 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.188, A:H.247, A:E.251 MG.3: 2 residues within 4Å: Chain A: V.406, H.462 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.462

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

SO4.4: 3 residues within 4Å: Chain A: D.281, H.282, T.283 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.283, A:T.283 Water bridges: A:D.102 Salt bridges: A:H.282 SO4.5: 2 residues within 4Å: Chain A: A.234, R.236 4 PLIP interactions: 4 interactions with chain A Water bridges: A:L.235, A:L.235, A:R.236 Salt bridges: A:R.236 SO4.6: 4 residues within 4Å: Chain A: S.131, E.132, R.133, L.134 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.131, A:R.133, A:L.134 Water bridges: A:E.132 SO4.7: 4 residues within 4Å: Chain A: G.159, E.160, R.161 Ligands: SO4.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.160, A:E.160, A:E.160, A:R.161 SO4.9: 2 residues within 4Å: Chain A: L.193, N.195 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.195, A:N.195 SO4.10: 4 residues within 4Å: Chain A: S.68, F.69, G.70, R.93 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.70 Water bridges: A:T.71 SO4.11: 3 residues within 4Å: Chain A: H.158, E.168 Ligands: SO4.7 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.168 Salt bridges: A:H.158

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 2 residues within 4Å: Chain A: G.267, G.268 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.268, A:G.268

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.12: 8 residues within 4Å: Chain A: G.368, A.373, Q.374, W.376, S.377, E.408, Y.423, E.430 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.374 Water bridges: A:S.377, A:E.430 Salt bridges: A:E.408, A:E.430

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sauvage, E. et al., Crystal Structures of R39-Imipenem Acyl-Enzyme. To be Published

Release Date

2013-03-20

Peptides

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

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