SMTL ID : 6kxi.1

Crystal Structure Of NDM-1 Metallo-beta-lactamase In Complex With Inhibitor NO9

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-dimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.96, H.98, D.100, H.165, C.184 Ligands: ZN.2, NO9.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.96, A:H.98, A:H.165 ZN.2: 5 residues within 4Å: Chain A: D.100, C.184, H.226 Ligands: ZN.1, NO9.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.100, A:C.184, A:H.226 ZN.3: 5 residues within 4Å: Chain A: H.3, E.128, D.199 Chain B: E.203, H.204 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.3, A:E.128, A:D.199, B:E.203, B:E.203 ZN.8: 7 residues within 4Å: Chain B: H.96, H.98, D.100, H.165, C.184 Ligands: ZN.9, NO9.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.96, B:H.98, B:H.165 ZN.9: 5 residues within 4Å: Chain B: D.100, C.184, H.226 Ligands: ZN.8, NO9.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.100, B:C.184, B:H.226 ZN.10: 4 residues within 4Å: Chain A: E.203, H.204 Chain B: E.128, D.199 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:E.203, A:E.203, B:E.128, B:E.128, B:D.199

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

SO4.4: 3 residues within 4Å: Chain A: R.210, T.236, R.240 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.210, A:R.240 SO4.5: 3 residues within 4Å: Chain A: Q.134, H.135, S.136 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.136, A:S.136 Water bridges: A:H.135, A:S.136 Salt bridges: A:H.135 SO4.6: 4 residues within 4Å: Chain A: F.216, P.217, K.218, A.219 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.216, A:K.218, A:A.219 Water bridges: A:D.175, A:T.177, A:K.218 Salt bridges: A:K.218 SO4.11: 3 residues within 4Å: Chain B: A.191, K.192, S.193 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.192, B:S.193, B:S.193 Water bridges: B:G.195 Salt bridges: B:K.192

2 x NO9: 2,5-dimethyl-4-sulfamoyl-furan-3-carboxylic acid(Non-covalent)

NO9.7: 15 residues within 4Å: Chain A: M.4, M.43, W.69, H.96, H.98, D.100, H.165, C.184, K.187, L.194, G.195, N.196, H.226 Ligands: ZN.1, ZN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.69, A:N.196 Hydrogen bonds: A:N.196, A:N.196 Salt bridges: A:H.165, A:K.187, A:H.226 pi-Cation interactions: A:H.226 NO9.12: 14 residues within 4Å: Chain B: M.43, W.69, H.96, H.98, D.100, H.165, C.184, K.187, L.194, G.195, N.196, H.226 Ligands: ZN.8, ZN.9 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.69, B:N.196 Hydrogen bonds: B:N.196, B:N.196 Salt bridges: B:H.165, B:K.187, B:H.226 pi-Cation interactions: B:H.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wachino, J.I. et al., Sulfamoyl Heteroarylcarboxylic Acids as Promising Metallo-beta-Lactamase Inhibitors for Controlling Bacterial Carbapenem Resistance. Mbio (2020)

Release Date

2020-02-19

Peptides

Beta-lactamase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-lactamase

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