SMTL ID : 4rl2.1

Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins

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: 3S3.3 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:H.96, A:H.98, A:H.165, 3S3.3, H2O.7 ZN.2: 4 residues within 4Å: Chain A: D.100, C.184, H.226 Ligands: 3S3.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.100, A:C.184, A:H.226, H2O.7 ZN.4: 4 residues within 4Å: Chain B: H.96, H.98, H.165 Ligands: 3S3.6 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:H.96, B:H.98, B:H.165, 3S3.6, H2O.16 ZN.5: 4 residues within 4Å: Chain B: D.100, C.184, H.226 Ligands: 3S3.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.100, B:C.184, B:H.226, H2O.16

2 x 3S3: (1R)-2-({(R)-carboxy[(2R,5S)-4-carboxy-5-methyl-5,6-dihydro-2H-1,3-thiazin-2-yl]methyl}amino)-2-oxo-1-phenylethanaminium(Non-covalent)

3S3.3: 20 residues within 4Å: Chain A: L.41, M.43, V.49, W.69, H.98, Q.99, D.100, H.165, C.184, K.187, G.195, N.196, H.226 Chain B: T.10, M.43, P.44, G.45, F.46 Ligands: ZN.1, ZN.2 19 PLIP interactions: 5 interactions with chain B, 14 interactions with chain A Hydrophobic interactions: B:T.10, B:F.46, B:F.46, B:F.46, A:L.41, A:W.69, A:W.69, A:N.196 Hydrogen bonds: B:G.45, A:Q.99, A:Q.99, A:D.100, A:N.196, A:N.196 Salt bridges: A:H.98, A:H.165, A:H.165, A:K.187, A:H.226 3S3.6: 19 residues within 4Å: Chain A: T.10, P.44, G.45, F.46 Chain B: L.41, M.43, V.49, W.69, H.98, Q.99, D.100, H.165, C.184, K.187, G.195, N.196, H.226 Ligands: ZN.4, ZN.5 18 PLIP interactions: 14 interactions with chain B, 4 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 Water bridges: B:Q.99 Salt bridges: B:H.98, B:H.165, B:H.165, B:K.187, B:H.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, H. et al., Structural and Mechanistic Insights into NDM-1 Catalyzed Hydrolysis of Cephalosporins. J.Am.Chem.Soc. (2014)

Release Date

2014-11-19

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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