SMTL ID : 4hl2.3 (2 other biounits)

New Delhi Metallo-beta-Lactamase-1 1.05 A structure Complexed with Hydrolyzed Ampicillin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

homo-dimer

Ligands

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)

ZZ7.1: 15 residues within 4Å: Chain A: L.38, M.40, W.66, H.95, Q.96, D.97, H.162, C.181, K.184, L.191, G.192, N.193, H.223 Ligands: ZN.2, ZN.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.38, A:W.66 Hydrogen bonds: A:Q.96, A:Q.96, A:D.97, A:N.193, A:N.193 Water bridges: A:Q.96 Salt bridges: A:H.95, A:H.162, A:H.162, A:K.184, A:H.223 ZZ7.9: 15 residues within 4Å: Chain B: L.38, M.40, W.66, H.95, Q.96, D.97, H.162, C.181, K.184, L.191, G.192, N.193, H.223 Ligands: ZN.10, ZN.11 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.38, B:W.66, B:N.193 Hydrogen bonds: B:Q.96, B:Q.96, B:D.97, B:N.193, B:N.193 Water bridges: B:Q.96 Salt bridges: B:H.95, B:H.162, B:H.162, B:K.184, B:H.223

5 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.93, H.95, H.162 Ligands: ZZ7.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.93, A:H.95, A:H.162, H2O.12 ZN.3: 4 residues within 4Å: Chain A: D.97, C.181, H.223 Ligands: ZZ7.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.97, A:C.181, A:H.223 ZN.10: 4 residues within 4Å: Chain B: H.93, H.95, H.162 Ligands: ZZ7.9 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.93, B:H.95, B:H.162, H2O.23 ZN.11: 4 residues within 4Å: Chain B: D.97, C.181, H.223 Ligands: ZZ7.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.97, B:C.181, B:H.223 ZN.12: 4 residues within 4Å: Chain A: E.200, H.201 Chain B: E.125, D.196 5 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.200, B:E.125, B:E.125, B:D.196, H2O.24

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

EDO.4: 3 residues within 4Å: Chain A: P.85, V.86, A.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.86 Water bridges: A:G.109 EDO.5: 2 residues within 4Å: Chain A: N.30, G.173 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.30, A:G.173 EDO.6: 2 residues within 4Å: Chain A: D.55, G.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.55 Water bridges: A:G.57 EDO.7: 2 residues within 4Å: Chain A: R.207, T.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.207 EDO.8: 7 residues within 4Å: Chain A: S.164, D.196, A.197 Chain B: S.164, D.196, A.197, D.198 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.197 Water bridges: A:S.164, B:S.164, B:S.164, B:T.199 EDO.13: 3 residues within 4Å: Chain B: R.207, A.208, A.211 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.204 EDO.14: 3 residues within 4Å: Chain B: N.193, L.194, G.195 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.193, B:N.193, B:G.195 Water bridges: B:L.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., New Delhi Metallo-beta-Lactamase-1 1.05 A structure Complexed with Hydrolyzed Ampicillin. To be Published

Release Date

2012-12-12

Peptides

Beta-lactamase NDM-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-lactamase NDM-1

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