SMTL ID : 9u9c.1

Crystal structure of NDM-1 in complex with hydrolyzed amoxicillin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.92, H.94, H.161 Ligands: 01.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.92, A:H.94, A:H.161, H2O.1 ZN.2: 4 residues within 4Å: Chain A: D.96, C.180, H.222 Ligands: 01.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.96, A:C.180, A:H.222, H2O.1 ZN.4: 4 residues within 4Å: Chain A: H.94, E.124, D.195 Chain B: E.199 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.199, B:E.199, A:E.124, A:D.195, H2O.5 ZN.5: 4 residues within 4Å: Chain B: H.92, H.94, H.161 Ligands: 01.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.92, B:H.94, B:H.161, H2O.14 ZN.6: 4 residues within 4Å: Chain B: D.96, C.180, H.222 Ligands: 01.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.96, B:C.180, B:H.222, H2O.14

2 x 01: (2~{R},4~{S})-2-[(1~{R})-1-[[(2~{R})-2-azanyl-2-(4-hydroxyphenyl)ethanoyl]amino]-2-oxidanyl-2-oxidanylidene-ethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid

01.3: 16 residues within 4Å: Chain A: I.7, L.37, M.39, V.45, W.65, H.94, Q.95, D.96, H.161, C.180, K.183, G.191, N.192, H.222 Ligands: ZN.1, ZN.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.37, A:W.65, A:N.192 Hydrogen bonds: A:Q.95, A:Q.95, A:D.96, A:N.192, A:N.192 Salt bridges: A:H.94, A:H.161, A:H.161, A:K.183, A:H.222 01.7: 17 residues within 4Å: Chain B: I.7, L.37, M.39, V.45, W.65, H.94, Q.95, D.96, H.161, C.180, K.183, L.190, G.191, N.192, H.222 Ligands: ZN.5, ZN.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.65, B:N.192 Hydrogen bonds: B:Q.95, B:Q.95, B:D.96, B:N.192, B:N.192 Salt bridges: B:H.94, B:H.161, B:H.161, B:K.183, B:H.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, X. et al., Crystal structure reveals the hydrophilic R1 group impairs NDM-1-ligand binding via water penetration at L3. J Struct Biol X (2025)

Release Date

2025-07-09

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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