SMTL ID : 6cac.4 (3 other biounits)

Crystal structure of NDM-1 metallo-beta-lactamase harboring an insertion of a Pro residue in L3 loop

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.85, H.87, D.89, H.154 Ligands: CD.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.85, A:H.87, A:H.154, H2O.1

1 x CD: CADMIUM ION(Non-covalent)

CD.2: 4 residues within 4Å: Chain A: D.89, C.173, H.215 Ligands: ZN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.89, A:C.173, A:H.215, H2O.1, H2O.5

1 x NI: NICKEL (II) ION(Non-covalent)

NI.3: 1 residues within 4Å: Chain A: H.226 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.226

1 x CO: COBALT (II) ION(Non-covalent)

CO.4: 2 residues within 4Å: Chain A: E.117, D.188 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.117, A:E.117, A:D.188, A:D.188, H2O.7

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 2 residues within 4Å: Chain A: D.60, D.95 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.60, A:D.95, H2O.5

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

SO4.6: 4 residues within 4Å: Chain A: F.205, P.206, K.207, A.208 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.207, A:A.208 Water bridges: A:D.164, A:A.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Palacios, A.R. et al., The Reaction Mechanism of Metallo-beta-Lactamases Is Tuned by the Conformation of an Active-Site Mobile Loop. Antimicrob. Agents Chemother. (2019)

Release Date

2018-10-17

Peptides

Metallo-beta-lactamase type 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Metallo-beta-lactamase type 2

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