SMTL ID : 6kzl.1

Crystal Structure Of NDM-1 Metallo-beta-lactamase In Complex With Inhibitor X2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 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, E1C.9 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, E1C.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.100, A:C.184, A:H.226 ZN.3: 4 residues within 4Å: Chain A: H.3, E.128, D.199 Chain B: E.203 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.10: 7 residues within 4Å: Chain B: H.96, H.98, D.100, H.165, C.184 Ligands: ZN.11, E1C.13 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.96, B:H.98, B:H.165 ZN.11: 5 residues within 4Å: Chain B: D.100, C.184, H.226 Ligands: ZN.10, E1C.13 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.100, B:C.184, B:H.226 ZN.12: 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

5 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: 1 residues within 4Å: Chain A: K.192 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.190 Salt bridges: A:K.192 SO4.6: 1 residues within 4Å: Chain A: R.232 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.213, A:R.232 Salt bridges: A:R.232 SO4.7: 4 residues within 4Å: Chain A: Q.29, P.32, W.35, R.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.29 Salt bridges: A:R.57 SO4.8: 3 residues within 4Å: Chain A: Q.134, H.135, S.136 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.134, A:S.136 Water bridges: A:H.135, A:S.136 Salt bridges: A:H.135

2 x E1C: 2,5-diethyl-1-methyl-4-sulfamoyl-pyrrole-3-carboxylic acid(Non-covalent)

E1C.9: 14 residues within 4Å: Chain A: M.4, M.43, 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 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: 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 E1C.13: 13 residues within 4Å: Chain B: V.49, H.96, H.98, D.100, H.165, C.184, K.187, L.194, G.195, N.196, H.226 Ligands: ZN.10, ZN.11 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.49, B:N.196, B:H.226 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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