SMTL ID : 4hl1.3 (2 other biounits)

Crystal Structure of New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Ampicillin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 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: 14 residues within 4Å: Chain A: 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: CD.3, CL.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.95, A:Q.96, A:D.97, A:N.193 Salt bridges: A:H.162, A:K.184, A:H.223 ZZ7.6: 13 residues within 4Å: Chain B: W.66, H.95, Q.96, D.97, H.162, C.181, K.184, L.191, G.192, N.193, H.223 Ligands: CD.8, CL.10 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:N.193 Hydrogen bonds: B:Q.96, B:D.97, B:N.193 Salt bridges: B:H.162, B:K.184, B:H.223

6 x CD: CADMIUM ION(Non-covalent)

CD.2: 4 residues within 4Å: Chain A: H.93, H.95, H.162 Ligands: CL.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.93, A:H.95, A:H.162, H2O.4 CD.3: 4 residues within 4Å: Chain A: D.97, C.181, H.223 Ligands: ZZ7.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.97, A:C.181, A:H.223, H2O.4 CD.4: 4 residues within 4Å: Chain A: H.95, E.125, D.196 Chain B: E.200 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.200, B:E.200, A:D.196, H2O.1, H2O.12 CD.7: 4 residues within 4Å: Chain B: H.93, H.95, H.162 Ligands: CL.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.93, B:H.95, B:H.162, H2O.18 CD.8: 4 residues within 4Å: Chain B: D.97, C.181, H.223 Ligands: ZZ7.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.97, B:C.181, B:H.223, H2O.18 CD.9: 4 residues within 4Å: Chain A: E.200 Chain B: H.95, E.125, D.196 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:E.125, B:E.125, B:D.196, A:E.200, H2O.12

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

CL.5: 5 residues within 4Å: Chain A: H.95, H.162, N.193 Ligands: ZZ7.1, CD.2 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: H.95, H.162, N.193 Ligands: ZZ7.6, CD.7 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and 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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