SMTL ID : 4ram.3 (2 other biounits)

Crystal Structure of New Delhi Metallo-beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

7 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.97, C.181, H.223 Ligands: PNM.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.97, A:C.181, A:H.223, H2O.7 ZN.2: 4 residues within 4Å: Chain A: H.93, H.95, H.162 Ligands: PNM.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.93, A:H.95, A:H.162, H2O.7 ZN.3: 4 residues within 4Å: Chain A: E.125, D.196 Chain B: E.200 Ligands: CL.5 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:E.200, B:E.200, A:E.125, A:E.125, A:D.196 ZN.6: 4 residues within 4Å: Chain B: D.97, C.181, H.223 Ligands: PNM.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.97, B:C.181, B:H.223, H2O.13 ZN.7: 4 residues within 4Å: Chain B: H.93, H.95, H.162 Ligands: PNM.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.93, B:H.95, B:H.162, H2O.13 ZN.8: 4 residues within 4Å: Chain A: E.200 Chain B: E.125, D.196 Ligands: CL.11 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.125, B:E.125, B:D.196, A:E.200, A:E.200 ZN.10: 1 residues within 4Å: Chain B: H.132 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.132, H2O.8, H2O.10, H2O.14

2 x PNM: OPEN FORM - PENICILLIN G(Non-covalent)

PNM.4: 14 residues within 4Å: Chain A: L.38, V.40, W.66, H.95, Q.96, D.97, H.162, C.181, K.184, G.192, N.193, H.223 Ligands: ZN.1, ZN.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.38, A:V.40, A:Q.96, A:N.193 Hydrogen bonds: A:Q.96, A:D.97, A:N.193, A:N.193 Salt bridges: A:H.162, A:K.184, A:H.223 pi-Stacking: A:W.66 PNM.9: 13 residues within 4Å: Chain B: L.38, W.66, H.95, Q.96, D.97, H.162, C.181, K.184, G.192, N.193, H.223 Ligands: ZN.6, ZN.7 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.38, B:Q.96, B:N.193 Hydrogen bonds: B:Q.96, B:D.97, B:N.193, B:N.193 Salt bridges: B:H.162, B:K.184, B:H.223

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

CL.5: 4 residues within 4Å: Chain A: E.125, D.196 Chain B: E.200 Ligands: ZN.3 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: E.200 Chain B: E.125, D.196 Ligands: ZN.8 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of New Delhi Metallo-beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Penicillin G. To be Published

Release Date

2014-09-24

Peptides

Beta-lactamase NDM-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-lactamase NDM-1

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