SMTL ID : 4zi6.1

Crystal structure of leucine aminopeptidase from Helicobacter pylori

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: K.264, D.269, D.287, E.348 Ligands: ZN.2, BCT.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.269, A:D.287, A:E.348, H2O.2, H2O.9 ZN.2: 5 residues within 4Å: Chain A: D.269, K.276, D.346, E.348 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.269, A:D.346, A:D.346, A:E.348, H2O.2 ZN.5: 6 residues within 4Å: Chain B: K.264, D.269, D.287, E.348 Ligands: ZN.6, BCT.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.269, B:D.287, B:E.348, H2O.19, H2O.22 ZN.6: 5 residues within 4Å: Chain B: D.269, K.276, D.346, E.348 Ligands: ZN.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.269, B:D.346, B:D.346, B:E.348, H2O.22 ZN.9: 6 residues within 4Å: Chain C: K.264, D.269, D.287, E.348 Ligands: ZN.10, BCT.11 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.269, C:D.287, C:E.348, H2O.30, H2O.38 ZN.10: 5 residues within 4Å: Chain C: D.269, K.276, D.346, E.348 Ligands: ZN.9 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.269, C:D.346, C:D.346, C:E.348, H2O.30 ZN.13: 6 residues within 4Å: Chain D: K.264, D.269, D.287, E.348 Ligands: ZN.14, BCT.15 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.287, D:D.287, D:E.348, H2O.45, H2O.51 ZN.14: 5 residues within 4Å: Chain D: D.269, K.276, D.346, E.348 Ligands: ZN.13 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.269, D:D.346, D:D.346, D:E.348, H2O.45 ZN.17: 6 residues within 4Å: Chain E: K.264, D.269, D.287, E.348 Ligands: ZN.18, BCT.19 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.269, E:D.287, E:E.348, H2O.58, H2O.64 ZN.18: 5 residues within 4Å: Chain E: D.269, K.276, D.346, E.348 Ligands: ZN.17 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.269, E:D.346, E:D.346, E:E.348, H2O.65 ZN.21: 6 residues within 4Å: Chain F: K.264, D.269, D.287, E.348 Ligands: ZN.22, BCT.23 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.269, F:D.287, F:E.348, H2O.73, H2O.79 ZN.22: 5 residues within 4Å: Chain F: D.269, K.276, D.346, E.348 Ligands: ZN.21 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.269, F:D.346, F:D.346, F:E.348, H2O.73

6 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.3: 8 residues within 4Å: Chain A: K.264, D.346, A.347, E.348, G.349, R.350, L.374 Ligands: ZN.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.348, A:G.349, A:R.350, A:R.350, A:R.350 BCT.7: 8 residues within 4Å: Chain B: K.264, D.346, A.347, E.348, G.349, R.350, L.374 Ligands: ZN.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.264, B:G.349, B:R.350, B:L.374 BCT.11: 8 residues within 4Å: Chain C: K.264, D.346, A.347, E.348, G.349, R.350, L.374 Ligands: ZN.9 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.264, C:G.349, C:R.350, C:L.374 BCT.15: 8 residues within 4Å: Chain D: K.264, D.346, A.347, E.348, G.349, R.350, L.374 Ligands: ZN.13 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.349, D:R.350, D:R.350, D:R.350 BCT.19: 8 residues within 4Å: Chain E: K.264, D.346, A.347, E.348, G.349, R.350, L.374 Ligands: ZN.17 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:E.348, E:G.349, E:R.350, E:R.350, E:R.350 BCT.23: 8 residues within 4Å: Chain F: K.264, D.346, A.347, E.348, G.349, R.350, L.374 Ligands: ZN.21 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:G.349, F:R.350, F:R.350, F:R.350

6 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: A.467, G.468, Y.471 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.467, A:Y.471 NA.8: 3 residues within 4Å: Chain B: A.467, G.468, Y.471 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.468, B:Y.471 NA.12: 3 residues within 4Å: Chain C: A.467, G.468, Y.471 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.467, C:Y.471 Water bridges: C:E.384 NA.16: 3 residues within 4Å: Chain D: A.467, G.468, Y.471 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.467, D:Y.471 NA.20: 3 residues within 4Å: Chain E: A.467, G.468, Y.471 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:A.467, E:Y.471 Water bridges: E:T.283 NA.24: 3 residues within 4Å: Chain F: A.467, G.468, Y.471 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.471, F:Y.471

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Modak, J.K. et al., Structural basis for substrate specificity of Helicobacter pylori M17 aminopeptidase. Biochimie (2016)

Release Date

2015-12-23

Peptides

Cytosol aminopeptidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Cytosol aminopeptidase

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