SMTL ID : 4hky.2 (2 other biounits)

New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Faropenem

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x SFR: (2R)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-5-[(2R)-oxolan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylic acid(Non-covalent)

SFR.1: 11 residues within 4Å: Chain A: H.95, D.97, H.162, K.184, L.191, G.192, N.193, H.223 Ligands: FPM.2, CD.5, CD.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.193, A:N.193 Salt bridges: A:H.95, A:H.162, A:H.162, A:K.184, A:H.223

1 x FPM: (5R,6S)-6-(1-hydroxyethyl)-7-oxo-3-[(2R)-oxolan-2-yl]-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid(Non-covalent)

FPM.2: 14 residues within 4Å: Chain A: W.66, H.95, Q.96, D.97, H.162, C.181, K.184, L.191, G.192, N.193, H.223 Ligands: SFR.1, CD.5, CD.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.95 Hydrogen bonds: A:N.193, A:N.193 Salt bridges: A:H.162, A:K.184, A:H.223

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: R.5 No protein-ligand interaction detected (PLIP) GOL.4: 2 residues within 4Å: Chain A: R.5, R.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.5, A:R.5, A:R.18, A:R.18

3 x CD: CADMIUM ION(Non-covalent)

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

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

CL.8: 4 residues within 4Å: Chain A: F.213, P.214, K.215, A.216 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: K.189 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Faropenem. To be Published

Release Date

2013-01-23

Peptides

Beta-lactamase NDM-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Beta-lactamase NDM-1

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