SMTL ID : 5ypk.7 (7 other biounits)

Crystal structure of NDM-1 bound to hydrolyzed imipenem representing an EI2 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.92, H.94, H.161 Ligands: ZN.2, HIW.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.92, A:H.94, A:H.161 ZN.2: 5 residues within 4Å: Chain A: D.96, C.180, H.222 Ligands: ZN.1, HIW.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.96, A:C.180, A:H.222

1 x HIW: (2R,4S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-[(2-{[(Z)-iminomethyl]amino}ethyl)sulfanyl]-3,4-dihydro-2H-pyrrole-5-ca rboxylic acid(Non-covalent)

HIW.3: 15 residues within 4Å: Chain A: V.45, W.65, H.92, H.94, Q.95, D.96, H.161, C.180, K.183, S.189, G.191, N.192, H.222 Ligands: ZN.1, ZN.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.65, A:W.65 Hydrogen bonds: A:Q.95, A:D.96, A:D.96, A:N.192, A:N.192 Water bridges: A:S.189 Salt bridges: A:H.94, A:H.161, A:H.161, A:K.183, A:H.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, H. et al., The mechanism of NDM-1-catalyzed carbapenem hydrolysis is distinct from that of penicillin or cephalosporin hydrolysis. Nat Commun (2017)

Release Date

2018-02-21

Peptides

Metallo-beta-lactamase NDM-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

Metallo-beta-lactamase NDM-1

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