SMTL ID : 3jru.1

Crystal structure of Leucyl Aminopeptidase (pepA) from Xoo0834,Xanthomonas oryzae pv. oryzae KACC10331

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-hexamer

Ligands

6 x CO3: CARBONATE ION(Non-functional Binders)

CO3.1: 6 residues within 4Å: Chain A: K.262, A.345, E.346, G.347, R.348, L.372 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.262, A:R.348, A:R.348 CO3.5: 6 residues within 4Å: Chain B: K.262, A.345, E.346, G.347, R.348, L.372 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.346, B:G.347, B:R.348, B:L.372 CO3.9: 6 residues within 4Å: Chain C: K.262, A.345, E.346, G.347, R.348, L.372 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.262, C:R.348, C:R.348 CO3.13: 6 residues within 4Å: Chain D: K.262, A.345, E.346, G.347, R.348, L.372 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.346, D:G.347, D:R.348, D:L.372 CO3.17: 6 residues within 4Å: Chain E: K.262, A.345, E.346, G.347, R.348, L.372 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.262, E:R.348, E:R.348 CO3.21: 6 residues within 4Å: Chain F: K.262, A.345, E.346, G.347, R.348, L.372 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:E.346, F:G.347, F:R.348, F:L.372

12 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: K.262, D.267, D.285, E.346 Ligands: ZN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.267, A:D.285, A:E.346 ZN.3: 5 residues within 4Å: Chain A: D.267, K.274, D.344, E.346 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.267, A:D.344, A:D.344, A:E.346, H2O.2 ZN.6: 4 residues within 4Å: Chain B: D.267, D.344, E.346 Ligands: ZN.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.267, B:D.344, B:D.344, B:E.346 ZN.7: 5 residues within 4Å: Chain B: K.262, D.267, D.285, E.346 Ligands: ZN.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.285, B:E.346 ZN.10: 5 residues within 4Å: Chain C: K.262, D.267, D.285, E.346 Ligands: ZN.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.267, C:D.285, C:E.346 ZN.11: 5 residues within 4Å: Chain C: D.267, K.274, D.344, E.346 Ligands: ZN.10 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.267, C:D.344, C:D.344, C:E.346, H2O.29 ZN.14: 4 residues within 4Å: Chain D: D.267, D.344, E.346 Ligands: ZN.15 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.267, D:D.344, D:D.344, D:E.346 ZN.15: 5 residues within 4Å: Chain D: K.262, D.267, D.285, E.346 Ligands: ZN.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.285, D:E.346 ZN.18: 5 residues within 4Å: Chain E: K.262, D.267, D.285, E.346 Ligands: ZN.19 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.267, E:D.285, E:E.346 ZN.19: 5 residues within 4Å: Chain E: D.267, K.274, D.344, E.346 Ligands: ZN.18 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.267, E:D.344, E:D.344, E:E.346, H2O.56 ZN.22: 4 residues within 4Å: Chain F: D.267, D.344, E.346 Ligands: ZN.23 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.267, F:D.344, F:D.344, F:E.346 ZN.23: 5 residues within 4Å: Chain F: K.262, D.267, D.285, E.346 Ligands: ZN.22 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.285, F:E.346

6 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.320 Chain C: D.320 Chain E: D.320 Ligands: CA.12, CA.20 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:D.320, A:D.320, H2O.4, H2O.30, H2O.57 CA.8: 5 residues within 4Å: Chain B: D.320 Chain D: D.320 Chain F: D.320 Ligands: CA.16, CA.24 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: B:D.320, D:D.320, H2O.21, H2O.48, H2O.75 CA.12: 5 residues within 4Å: Chain A: D.320 Chain C: D.320 Chain E: D.320 Ligands: CA.4, CA.20 5 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: E:D.320, C:D.320, H2O.4, H2O.30, H2O.57 CA.16: 5 residues within 4Å: Chain B: D.320 Chain D: D.320 Chain F: D.320 Ligands: CA.8, CA.24 5 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: F:D.320, D:D.320, H2O.21, H2O.48, H2O.75 CA.20: 5 residues within 4Å: Chain A: D.320 Chain C: D.320 Chain E: D.320 Ligands: CA.4, CA.12 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: A:D.320, E:D.320, H2O.4, H2O.30, H2O.57 CA.24: 5 residues within 4Å: Chain B: D.320 Chain D: D.320 Chain F: D.320 Ligands: CA.8, CA.16 5 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: F:D.320, B:D.320, H2O.21, H2O.48, H2O.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Natarajan, S. et al., Crystal structure of Leucyl Aminopeptidase (pepA) from Xoo0834,Xanthomonas oryzae pv. oryzae KACC10331. to be published

Release Date

2010-09-08

Peptides

Probable cytosol aminopeptidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
B

D
A

E
B

F
A

Probable cytosol aminopeptidase