SMTL ID : 5o2f.1

Crystal structure of NDM-1 in complex with hydrolyzed ampicillin - new refinement

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.96, H.98, H.165 Ligands: ZZ7.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.96, A:H.98, A:H.165, H2O.2 ZN.2: 4 residues within 4Å: Chain A: D.100, C.184, H.226 Ligands: ZZ7.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.100, A:C.184, A:H.226, H2O.2 ZN.10: 4 residues within 4Å: Chain B: H.96, H.98, H.165 Ligands: ZZ7.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.96, B:H.98, B:H.165, H2O.10 ZN.11: 4 residues within 4Å: Chain B: D.100, C.184, H.226 Ligands: ZZ7.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.100, B:C.184, B:H.226, H2O.10

2 x ZZ7: (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid(Non-covalent)

ZZ7.3: 18 residues within 4Å: Chain A: M.43, W.69, H.98, Q.99, D.100, H.165, C.184, K.187, L.194, G.195, N.196, H.226 Chain B: T.10, P.44, G.45, F.46 Ligands: ZN.1, ZN.2 18 PLIP interactions: 13 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:W.69, A:W.69, A:N.196, B:T.10, B:F.46, B:F.46, B:F.46 Hydrogen bonds: A:Q.99, A:Q.99, A:D.100, A:N.196, A:N.196, B:G.45 Salt bridges: A:H.98, A:H.165, A:H.165, A:K.187, A:H.226 ZZ7.12: 18 residues within 4Å: Chain A: T.10, P.44, G.45, F.46 Chain B: L.41, M.43, W.69, H.98, Q.99, D.100, H.165, C.184, K.187, G.195, N.196, H.226 Ligands: ZN.10, ZN.11 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.41, B:W.69, B:N.196, A:T.10, A:F.46, A:F.46 Hydrogen bonds: B:Q.99, B:Q.99, B:D.100, B:N.196, B:N.196, A:G.45, A:G.45 Water bridges: B:Q.99 Salt bridges: B:H.98, B:H.165, B:H.165, B:K.187, B:H.226

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: 2 residues within 4Å: Chain A: H.237, R.240 4 PLIP interactions: 4 interactions with chain A Water bridges: A:A.233, A:H.237 Salt bridges: A:H.237, A:R.240 SO4.6: 1 residues within 4Å: Chain A: R.246 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.246 SO4.13: 2 residues within 4Å: Chain B: P.126, G.129 No protein-ligand interaction detected (PLIP)

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

CL.7: 2 residues within 4Å: Chain A: M.4, G.5 Ligand excluded by PLIP

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 4 residues within 4Å: Chain A: K.192, S.193 Chain B: A.191, K.192 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.192, A:S.193, A:S.193, B:K.192 EDO.9: 2 residues within 4Å: Chain A: H.135, S.136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.135, A:S.136 Water bridges: A:Q.134, A:S.136 EDO.14: 2 residues within 4Å: Chain B: H.135, S.136 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.136 Water bridges: B:H.135, B:S.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raczynska, J.E. et al., A close look onto structural models and primary ligands of metallo-beta-lactamases. Drug Resist. Updat. (2018)

Release Date

2018-12-26

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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