SMTL ID : 3zr9.2 (1 other biounit)

Structure of New Delhi Metallo-Beta-lactamase 1 (NDM-1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-octamer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.81, H.83, D.85, H.150, C.169 Ligands: CD.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.81, A:H.83, A:H.150, H2O.2 ZN.8: 6 residues within 4Å: Chain B: H.81, H.83, D.85, H.150, C.169 Ligands: CD.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.81, B:H.83, B:H.150, H2O.7 ZN.15: 6 residues within 4Å: Chain C: H.81, H.83, D.85, H.150, C.169 Ligands: CD.18 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.81, C:H.83, C:H.150, H2O.11 ZN.22: 6 residues within 4Å: Chain D: H.81, H.83, D.85, H.150, C.169 Ligands: CD.25 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.81, D:H.83, D:H.150, H2O.16 ZN.29: 6 residues within 4Å: Chain E: H.81, H.83, D.85, H.150, C.169 Ligands: CD.32 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.81, E:H.83, E:H.150, H2O.20 ZN.36: 6 residues within 4Å: Chain F: H.81, H.83, D.85, H.150, C.169 Ligands: CD.39 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.81, F:H.83, F:H.150, H2O.24 ZN.43: 6 residues within 4Å: Chain G: H.81, H.83, D.85, H.150, C.169 Ligands: CD.46 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.81, G:H.83, G:H.150, H2O.29 ZN.50: 6 residues within 4Å: Chain H: H.81, H.83, D.85, H.150, C.169 Ligands: CD.53 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.81, H:H.83, H:H.150, H2O.33

8 x CO: COBALT (II) ION(Non-covalent)

CO.2: 3 residues within 4Å: Chain A: D.56, G.88, D.91 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.56, A:D.91, H2O.2, H2O.2, H2O.2, H2O.2 CO.9: 3 residues within 4Å: Chain B: D.56, G.88, D.91 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.56, B:D.91, H2O.6, H2O.6, H2O.6, H2O.7 CO.16: 3 residues within 4Å: Chain C: D.56, G.88, D.91 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.56, C:D.91, H2O.11, H2O.11, H2O.11, H2O.11 CO.23: 3 residues within 4Å: Chain D: D.56, G.88, D.91 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.56, D:D.91, H2O.15, H2O.15, H2O.15, H2O.16 CO.30: 3 residues within 4Å: Chain E: D.56, G.88, D.91 6 PLIP interactions: 2 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.56, E:D.91, H2O.19, H2O.19, H2O.20, H2O.20 CO.37: 3 residues within 4Å: Chain F: D.56, G.88, D.91 6 PLIP interactions: 2 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:D.56, F:D.91, H2O.24, H2O.24, H2O.24, H2O.25 CO.44: 3 residues within 4Å: Chain G: D.56, G.88, D.91 6 PLIP interactions: 2 interactions with chain G, 4 Ligand-Water interactions Metal complexes: G:D.56, G:D.91, H2O.28, H2O.28, H2O.28, H2O.29 CO.51: 3 residues within 4Å: Chain H: D.56, G.88, D.91 6 PLIP interactions: 2 interactions with chain H, 4 Ligand-Water interactions Metal complexes: H:D.56, H:D.91, H2O.33, H2O.33, H2O.33, H2O.34

32 x NI: NICKEL (II) ION(Non-covalent)

NI.3: 1 residues within 4Å: Chain A: H.189 Ligand excluded by PLIP NI.5: 3 residues within 4Å: Chain A: H.120 Chain B: H.120 Ligands: NI.12 Ligand excluded by PLIP NI.6: 2 residues within 4Å: Chain A: S.174, H.222 Ligand excluded by PLIP NI.7: 3 residues within 4Å: Chain A: E.131 Chain F: E.113, D.184 Ligand excluded by PLIP NI.10: 1 residues within 4Å: Chain B: H.189 Ligand excluded by PLIP NI.12: 3 residues within 4Å: Chain A: H.120 Chain B: H.120 Ligands: NI.5 Ligand excluded by PLIP NI.13: 2 residues within 4Å: Chain B: S.174, H.222 Ligand excluded by PLIP NI.14: 3 residues within 4Å: Chain B: E.131 Chain G: E.113, D.184 Ligand excluded by PLIP NI.17: 1 residues within 4Å: Chain C: H.189 Ligand excluded by PLIP NI.19: 3 residues within 4Å: Chain C: H.120 Chain D: H.120 Ligands: NI.26 Ligand excluded by PLIP NI.20: 2 residues within 4Å: Chain C: S.174, H.222 Ligand excluded by PLIP NI.21: 3 residues within 4Å: Chain C: E.131 Chain E: E.113, D.184 Ligand excluded by PLIP NI.24: 1 residues within 4Å: Chain D: H.189 Ligand excluded by PLIP NI.26: 3 residues within 4Å: Chain C: H.120 Chain D: H.120 Ligands: NI.19 Ligand excluded by PLIP NI.27: 2 residues within 4Å: Chain D: S.174, H.222 Ligand excluded by PLIP NI.28: 3 residues within 4Å: Chain D: E.131 Chain H: E.113, D.184 Ligand excluded by PLIP NI.31: 1 residues within 4Å: Chain E: H.189 Ligand excluded by PLIP NI.33: 3 residues within 4Å: Chain E: H.120 Chain G: H.120 Ligands: NI.47 Ligand excluded by PLIP NI.34: 2 residues within 4Å: Chain E: S.174, H.222 Ligand excluded by PLIP NI.35: 3 residues within 4Å: Chain A: E.113, D.184 Chain E: E.131 Ligand excluded by PLIP NI.38: 1 residues within 4Å: Chain F: H.189 Ligand excluded by PLIP NI.40: 3 residues within 4Å: Chain F: H.120 Chain H: H.120 Ligands: NI.54 Ligand excluded by PLIP NI.41: 2 residues within 4Å: Chain F: S.174, H.222 Ligand excluded by PLIP NI.42: 3 residues within 4Å: Chain C: E.113, D.184 Chain F: E.131 Ligand excluded by PLIP NI.45: 1 residues within 4Å: Chain G: H.189 Ligand excluded by PLIP NI.47: 3 residues within 4Å: Chain E: H.120 Chain G: H.120 Ligands: NI.33 Ligand excluded by PLIP NI.48: 2 residues within 4Å: Chain G: S.174, H.222 Ligand excluded by PLIP NI.49: 3 residues within 4Å: Chain D: E.113, D.184 Chain G: E.131 Ligand excluded by PLIP NI.52: 1 residues within 4Å: Chain H: H.189 Ligand excluded by PLIP NI.54: 3 residues within 4Å: Chain F: H.120 Chain H: H.120 Ligands: NI.40 Ligand excluded by PLIP NI.55: 2 residues within 4Å: Chain H: S.174, H.222 Ligand excluded by PLIP NI.56: 3 residues within 4Å: Chain B: E.113, D.184 Chain H: E.131 Ligand excluded by PLIP

8 x CD: CADMIUM ION(Non-covalent)

CD.4: 4 residues within 4Å: Chain A: D.85, C.169, H.211 Ligands: ZN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.85, A:C.169, A:H.211, H2O.2, H2O.4 CD.11: 4 residues within 4Å: Chain B: D.85, C.169, H.211 Ligands: ZN.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.85, B:C.169, B:H.211, H2O.7, H2O.8 CD.18: 4 residues within 4Å: Chain C: D.85, C.169, H.211 Ligands: ZN.15 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.85, C:C.169, C:H.211, H2O.11, H2O.13 CD.25: 4 residues within 4Å: Chain D: D.85, C.169, H.211 Ligands: ZN.22 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.85, D:C.169, D:H.211, H2O.16, H2O.17 CD.32: 4 residues within 4Å: Chain E: D.85, C.169, H.211 Ligands: ZN.29 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.85, E:C.169, E:H.211, H2O.20, H2O.22 CD.39: 4 residues within 4Å: Chain F: D.85, C.169, H.211 Ligands: ZN.36 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.85, F:C.169, F:H.211, H2O.25, H2O.26 CD.46: 4 residues within 4Å: Chain G: D.85, C.169, H.211 Ligands: ZN.43 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.85, G:C.169, G:H.211, H2O.29, H2O.31 CD.53: 4 residues within 4Å: Chain H: D.85, C.169, H.211 Ligands: ZN.50 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.85, H:C.169, H:H.211, H2O.34, H2O.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Green, V.L. et al., Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1). Acta Crystallogr.,Sect.F (2011)

Release Date

2011-06-29

Peptides

BETA-LACTAMASE NDM-1: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

BETA-LACTAMASE NDM-1

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