SMTL ID : 5ypi.8 (7 other biounits)

Crystal structure of NDM-1 bound to hydrolyzed imipenem representing an EI1 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 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, C.180 Ligands: 8YF.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.92, A:H.94, A:H.161 ZN.2: 4 residues within 4Å: Chain A: D.96, C.180, H.222 Ligands: 8YF.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.96, A:C.180, A:H.222, H2O.1

1 x 8YF: (2R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-(2-methanimidamidoethylsulfanyl)-2,3-dihydro-1H-pyrrole -5-carboxylic acid(Non-covalent)

8YF.3: 13 residues within 4Å: Chain A: W.65, H.94, D.96, H.161, C.180, K.183, K.188, S.189, G.191, N.192, H.222 Ligands: ZN.1, ZN.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.65, A:D.96 Hydrogen bonds: A:D.96, A:K.188, A:K.188, A:S.189, A:N.192, A:N.192 Water bridges: A:Q.95, A:K.183, A:K.183 Salt bridges: A:H.92, A:H.94, A:H.161, A:K.183, A:H.222

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

SO4.4: 1 residues within 4Å: Chain A: H.233 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.233

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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