SMTL ID : 3sfp.6 (5 other biounits)

Crystal Structure of the Mono-Zinc-boundform of New Delhi Metallo-beta-Lactamase-1 from Klebsiella pneumoniae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.87, H.89, H.156, C.175 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.87, A:H.89, A:H.156, H2O.2 ZN.7: 4 residues within 4Å: Chain B: H.87, H.89, H.156, C.175 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.87, B:H.89

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 11 residues within 4Å: Chain A: D.10, V.17, R.19, Q.27, T.29, Y.31, A.41, N.43, S.218, A.219, P.220 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.27, A:Y.31, A:N.43 Salt bridges: A:R.19 CIT.8: 10 residues within 4Å: Chain B: D.10, V.17, R.19, Q.27, T.29, N.43, H.217, S.218, A.219, P.220 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.10, B:Q.27, B:T.29, B:N.43 Salt bridges: B:R.19, B:R.19

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: H.228, R.231 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.228, A:R.231 SO4.9: 2 residues within 4Å: Chain B: R.201, R.231 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.201, B:R.231 SO4.10: 3 residues within 4Å: Chain B: T.227, H.228, R.231 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.227 Salt bridges: B:H.228, B:R.231

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: R.223, A.224, T.227 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.224, A:T.227, A:T.227 GOL.5: 8 residues within 4Å: Chain A: K.148, G.164, I.165, D.166, T.168, D.169, I.170, A.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.166 GOL.11: 4 residues within 4Å: Chain A: A.131, A.132 Chain B: H.126, S.127 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.126, B:S.127, B:S.127, A:A.132

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

CL.6: 2 residues within 4Å: Chain A: K.183, S.184 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Structure of Apo- and Monometalated Forms of NDM-1 A Highly Potent Carbapenem-Hydrolyzing Metallo-beta-Lactamase. Plos One (2011)

Release Date

2011-06-29

Peptides

Beta-lactamase NDM-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

Beta-lactamase NDM-1

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