SMTL ID : 8i8f.1

Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.120, H.122, H.189 Ligands: OL6.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.120, A:H.122, A:H.189, H2O.1 ZN.2: 4 residues within 4Å: Chain A: D.124, C.208, H.250 Ligands: OL6.3 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.124, A:C.208, A:H.250, H2O.1, OL6.3 ZN.4: 4 residues within 4Å: Chain B: H.120, H.122, H.189 Ligands: OL6.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.120, B:H.122, B:H.189, H2O.12 ZN.5: 4 residues within 4Å: Chain B: D.124, C.208, H.250 Ligands: OL6.6 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:D.124, B:C.208, B:H.250, OL6.6, H2O.12

2 x OL6: (2R,4S)-5,5-dimethyl-2-[(1R)-1-(2-naphthalen-1-yloxyethanoylamino)-2-oxidanyl-2-oxidanylidene-ethyl]-1,3-thiazolidine-4-carboxylic acid(Non-covalent)

OL6.3: 23 residues within 4Å: Chain A: I.35, L.65, M.67, F.70, V.73, W.93, H.122, Q.123, D.124, H.189, C.208, K.211, L.218, G.219, N.220, H.250 Chain B: T.34, P.68, G.69, F.70 Ligands: ZN.1, ZN.2, OL6.6 18 PLIP interactions: 13 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.65, A:V.73, A:W.93, A:N.220, B:T.34, B:F.70, B:F.70, B:F.70 Hydrogen bonds: A:Q.123, A:D.124, A:N.220, A:N.220, B:G.69 Salt bridges: A:H.122, A:H.189, A:H.189, A:K.211, A:H.250 OL6.6: 22 residues within 4Å: Chain A: T.34, P.68, G.69, F.70 Chain B: L.65, M.67, F.70, V.73, W.93, H.122, Q.123, D.124, H.189, C.208, K.211, L.218, G.219, N.220, H.250 Ligands: OL6.3, ZN.4, ZN.5 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:V.73, B:W.93, B:N.220, A:T.34, A:F.70, A:F.70 Hydrogen bonds: B:Q.123, B:D.124, B:N.220, B:N.220, A:G.69, A:G.69 Salt bridges: B:H.122, B:H.189, B:H.189, B:K.211, B:H.250

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, X. et al., Interplay between the beta-lactam side chain and an active-site mobile loop of NDM-1 in penicillin hydrolysis as a potential target for mechanism-based inhibitor design. Int.J.Biol.Macromol. (2024)

Release Date

2024-02-07

Peptides

Metallo beta lactamase NDM-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Metallo beta lactamase NDM-1

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