SMTL ID : 3h8f.1

High pH native structure of leucine aminopeptidase from Pseudomonas putida

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: K.267, D.272, D.290, E.351 Ligands: MN.2, BCT.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.272, A:D.290, A:E.351, H2O.4 ZN.5: 6 residues within 4Å: Chain B: K.267, D.272, D.290, E.351 Ligands: MN.6, BCT.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.272, B:D.290, B:E.351, H2O.8 ZN.9: 6 residues within 4Å: Chain C: K.267, D.272, D.290, E.351 Ligands: MN.10, BCT.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.272, C:D.290, C:E.351, H2O.14 ZN.13: 6 residues within 4Å: Chain D: K.267, D.272, D.290, E.351 Ligands: MN.14, BCT.16 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.272, D:D.290, D:E.351, H2O.19 ZN.17: 6 residues within 4Å: Chain E: K.267, D.272, D.290, E.351 Ligands: MN.18, BCT.20 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.272, E:D.290, E:E.351, H2O.23 ZN.21: 6 residues within 4Å: Chain F: K.267, D.272, D.290, E.351 Ligands: MN.22, BCT.24 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.272, F:D.290, F:E.351, H2O.27

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: D.272, K.279, D.349, E.351 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.272, A:D.349, A:D.349, A:E.351, H2O.4 MN.6: 4 residues within 4Å: Chain B: D.272, D.349, E.351 Ligands: ZN.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.272, B:D.349, B:D.349, B:E.351, H2O.8 MN.10: 5 residues within 4Å: Chain C: D.272, D.349, E.351 Ligands: ZN.9, BCT.12 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.272, C:D.349, C:D.349, C:E.351, H2O.14 MN.14: 5 residues within 4Å: Chain D: D.272, D.349, E.351 Ligands: ZN.13, BCT.16 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.272, D:D.349, D:D.349, D:E.351, H2O.19 MN.18: 5 residues within 4Å: Chain E: D.272, K.279, D.349, E.351 Ligands: ZN.17 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.272, E:D.349, E:D.349, E:E.351, H2O.23 MN.22: 5 residues within 4Å: Chain F: D.272, K.279, D.349, E.351 Ligands: ZN.21 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.272, F:D.349, F:D.349, F:E.351, H2O.27

6 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: L.189, G.190, L.192, C.197, K.288, M.291 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.189, A:G.190, A:L.192, A:K.288, H2O.1 K.7: 6 residues within 4Å: Chain B: L.189, G.190, L.192, C.197, K.288, M.291 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.189, B:G.190, B:L.192, B:K.288, H2O.8 K.11: 6 residues within 4Å: Chain C: L.189, G.190, L.192, C.197, K.288, M.291 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:L.189, C:G.190, C:L.192, C:K.288, H2O.14 K.15: 6 residues within 4Å: Chain D: L.189, G.190, L.192, C.197, K.288, M.291 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:L.189, D:G.190, D:L.192, H2O.15 K.19: 6 residues within 4Å: Chain E: L.189, G.190, L.192, C.197, K.288, M.291 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:L.189, E:G.190, E:L.192, E:K.288, H2O.21 K.23: 6 residues within 4Å: Chain F: L.189, G.190, L.192, C.197, K.288, M.291 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:L.189, F:G.190, F:L.192, H2O.24

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

BCT.4: 7 residues within 4Å: Chain A: K.267, A.350, E.351, G.352, R.353, L.377 Ligands: ZN.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.267, A:E.351, A:G.352, A:R.353, A:L.377 BCT.8: 9 residues within 4Å: Chain B: K.267, D.349, A.350, E.351, G.352, R.353, L.377, T.378 Ligands: ZN.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.350, B:E.351, B:G.352, B:L.377 BCT.12: 9 residues within 4Å: Chain C: K.267, D.349, A.350, E.351, G.352, R.353, L.377 Ligands: ZN.9, MN.10 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.351, C:G.352, C:R.353, C:R.353, C:R.353 BCT.16: 9 residues within 4Å: Chain D: K.267, D.349, A.350, E.351, G.352, R.353, L.377 Ligands: ZN.13, MN.14 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.351, D:R.353, D:R.353, D:R.353 BCT.20: 7 residues within 4Å: Chain E: K.267, A.350, E.351, G.352, R.353, L.377 Ligands: ZN.17 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:E.351, E:G.352, E:R.353, E:R.353, E:R.353 BCT.24: 8 residues within 4Å: Chain F: K.267, D.349, A.350, E.351, G.352, R.353, L.377 Ligands: ZN.21 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:E.351, F:R.353, F:R.353, F:R.353

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kale, A. et al., Crystal structure of the leucine aminopeptidase from Pseudomonas putida reveals the molecular basis for its enantioselectivity and broad substrate specificity. J.Mol.Biol. (2010)

Release Date

2010-04-14

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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