SMTL ID : 5o2e.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.92, H.94, H.161 Ligands: ZN.2, 3S0.4 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.92, A:H.94, A:H.161, H2O.2, 3S0.4 ZN.2: 5 residues within 4Å: Chain A: D.96, C.180, H.222 Ligands: ZN.1, 3S0.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.96, A:C.180, A:H.222, H2O.2 ZN.7: 5 residues within 4Å: Chain B: H.92, H.94, H.161 Ligands: ZN.8, 3S0.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.92, B:H.94, B:H.161, H2O.16 ZN.8: 5 residues within 4Å: Chain B: D.96, C.180, H.222 Ligands: ZN.7, 3S0.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.96, B:C.180, B:H.222, H2O.16

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

SO4.3: 1 residues within 4Å: Chain A: R.242 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.242

2 x 3S0: (2R,5S)-5-[(carbamoyloxy)methyl]-2-[(R)-carboxy{[(2Z)-2-(furan-2-yl)-2-(methoxyimino)acetyl]amino}methyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid(Non-covalent)

3S0.4: 19 residues within 4Å: Chain A: L.37, M.39, W.65, H.94, Q.95, D.96, E.124, H.161, C.180, K.183, G.191, N.192, H.222 Chain B: P.40, G.41, F.42 Ligands: ZN.1, ZN.2, UNL.5 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:N.192 Hydrogen bonds: A:Q.95, A:D.96, A:N.192, A:N.192, B:G.41, B:G.41 Salt bridges: A:H.94, A:H.161, A:H.161, A:K.183, A:H.222 3S0.9: 18 residues within 4Å: Chain A: P.40, G.41, F.42 Chain B: L.37, M.39, W.65, H.94, Q.95, D.96, H.161, C.180, K.183, G.191, N.192, H.222 Ligands: UNL.6, ZN.7, ZN.8 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:G.41, B:Q.95, B:D.96, B:N.192, B:N.192 Hydrophobic interactions: B:L.37 Salt bridges: B:H.94, B:H.161, B:H.161, B:K.183, B:H.222

2 x UNL: UNKNOWN LIGAND

UNL.5: 4 residues within 4Å: Chain A: I.7 Chain B: T.6, F.42 Ligands: 3S0.4 No protein-ligand interaction detected (PLIP) UNL.6: 4 residues within 4Å: Chain A: T.6, F.42 Chain B: I.7 Ligands: 3S0.9 No protein-ligand interaction detected (PLIP)

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

2018-12-26

Peptides

Metallo-beta-lactamase type 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Metallo-beta-lactamase type 2

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