SMTL ID : 5n0h.1 (1 other biounit)

Crystal structure of NDM-1 in complex with hydrolyzed meropenem - new refinement

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

8YL.1: 15 residues within 4Å: Chain A: V.45, W.65, H.92, H.94, Q.95, D.96, H.161, C.180, K.183, L.190, G.191, N.192, H.222 Ligands: ZN.2, ZN.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.45 Hydrogen bonds: A:D.96, A:N.192, A:N.192 Water bridges: A:K.183 Salt bridges: A:H.92, A:H.94, A:H.161, A:H.161, A:K.183, A:H.222

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.96, C.180, H.222 Ligands: 8YL.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.96, A:C.180, A:H.222, H2O.6 ZN.3: 4 residues within 4Å: Chain A: H.92, H.94, H.161 Ligands: 8YL.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.92, A:H.94, A:H.161, H2O.6

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: R.206, T.232, A.235, R.236 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.206, A:R.236, A:D.239 GOL.5: 9 residues within 4Å: Chain A: K.153, G.169, I.170, T.173, D.174, I.175, F.212, K.214, A.215 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.170, A:I.170, A:I.175, A:K.214 Water bridges: A:K.214

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

SO4.6: 4 residues within 4Å: Chain A: Q.79, E.80, I.81, N.82 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.79 Water bridges: A:N.82, A:N.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raczynska, J.E. et al., A close look onto structural models and primary ligands of metallo-beta-lactamases. Drug Resist. Updat. (2018)

Release Date

2017-04-05

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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