SMTL ID : 6twt.2 (1 other biounit)

Crystal structure of N-terminally truncated NDM-1 metallo-beta-lactamase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.95 Å

Oligo State

monomer

Ligands

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.1: 3 residues within 4Å: Chain A: R.207, T.233, R.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.237 Salt bridges: A:R.207, A:R.237

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: H.93, H.95, H.162 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.93, A:H.95, A:H.162, H2O.1, H2O.6 ZN.3: 3 residues within 4Å: Chain A: D.97, C.181, H.223 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.97, A:C.181, A:H.223, H2O.1, H2O.8

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain A: E.125, D.196 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.125, A:D.196, A:D.196, H2O.7, H2O.8 CA.5: 1 residues within 4Å: Chain A: G.151 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.151, H2O.4, H2O.6, H2O.8, H2O.10 CA.6: 2 residues within 4Å: Chain A: D.68, D.103 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.68, A:D.103, H2O.2, H2O.5, H2O.9

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 2 residues within 4Å: Chain A: H.132, S.133 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: F.213, P.214, K.215, A.216 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raczynska, J.E. et al., Flexible loops of New Delhi metallo-beta-lactamase modulate its activity towards different substrates. Int.J.Biol.Macromol. (2020)

Release Date

2020-05-13

Peptides

Metallo beta lactamase NDM-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Metallo beta lactamase NDM-1

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