SMTL ID : 6zyp.1 (1 other biounit)

Structure of NDM-1 with 2-Mercaptomethyl-thiazolidine L-anti-1b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 8 residues within 4Å: Chain A: H.94, D.98, K.99, C.182, S.223, H.224 Ligands: ZN.2, QT2.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.98, A:C.182, A:H.224 ZN.2: 6 residues within 4Å: Chain A: H.94, H.96, H.163, C.182 Ligands: ZN.1, QT2.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.94, A:H.96, A:H.163

1 x QT2: (2~{S},4~{R})-2-ethoxycarbonyl-5,5-dimethyl-2-(sulfanylmethyl)-1,3-thiazolidine-4-carboxylic acid(Non-covalent)

QT2.3: 15 residues within 4Å: Chain A: I.9, L.39, M.41, V.47, W.67, H.94, H.96, Q.97, D.98, H.163, C.182, N.194, H.224 Ligands: ZN.1, ZN.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.97, A:D.98, A:N.194, A:N.194

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

SO4.4: 3 residues within 4Å: Chain A: Q.132, H.133, S.134 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.132, A:S.134 Water bridges: A:H.133, A:H.133, A:S.134 Salt bridges: A:H.133 SO4.5: 3 residues within 4Å: Chain A: R.208, T.234, R.238 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.208, A:R.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rossi, M.A. et al., 2-Mercaptomethyl-thiazolidines use conserved aromatic-S interactions to achieve broad-range inhibition of metallo-beta-lactamases. Chem Sci (2021)

Release Date

2021-01-20

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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