SMTL ID : 5zgp.1 (1 other biounit)

Crystal structure of NDM-1 at pH6.2 (Bis-Tris) in complex with hydrolyzed ampicillin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.92, H.94, H.161 Ligands: ZZ7.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.92, A:H.94, A:H.161, H2O.1 ZN.2: 4 residues within 4Å: Chain A: D.96, C.180, H.222 Ligands: ZZ7.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.96, A:C.180, A:H.222

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

PEG.3: 5 residues within 4Å: Chain A: P.84, V.85, A.107, G.108, I.109 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.85, A:G.108

1 x ZZ7: (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid(Non-covalent)

ZZ7.4: 15 residues within 4Å: Chain A: L.37, M.39, W.65, H.94, Q.95, D.96, H.161, C.180, K.183, L.190, G.191, N.192, H.222 Ligands: ZN.1, ZN.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.37, A:W.65, A:N.192 Hydrogen bonds: A:Q.95, A:Q.95, A:D.96, A:N.192, A:N.192 Water bridges: A:H.94, A:Q.95 Salt bridges: A:H.94, A:H.161, A:H.161, A:K.183, A:H.222

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: I.170, D.171, G.172, T.173, I.175, K.214, A.215 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.171, A:D.171, A:G.172, A:T.173, A:K.214 Water bridges: A:A.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, H. et al., Active-Site Conformational Fluctuations Promote the Enzymatic Activity of NDM-1. Antimicrob. Agents Chemother. (2018)

Release Date

2018-08-22

Peptides

Metallo-beta-lactamase type 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Metallo-beta-lactamase type 2

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