SMTL ID : 1xfo.1

Crystal Structure of an archaeal aminopeptidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-12-mer

Ligands

24 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain C: H.72, D.186, D.187, E.216, D.239 Ligands: ZN.5 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.72, C:D.186, C:D.239, C:D.239, H2O.379 ZN.2: 6 residues within 4Å: Chain A: H.72, D.186, D.187, E.216, D.239 Ligands: ZN.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.72, A:D.186, A:D.239, A:D.239, H2O.83 ZN.3: 6 residues within 4Å: Chain D: H.72, D.186, D.187, E.216, D.239 Ligands: ZN.4 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.72, D:D.186, D:D.239, D:D.239, H2O.532 ZN.4: 4 residues within 4Å: Chain D: D.186, E.217, H.327 Ligands: ZN.3 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.186, D:E.217, D:E.217, D:H.327, H2O.532 ZN.5: 4 residues within 4Å: Chain C: D.186, E.217, H.327 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.186, C:E.217, C:E.217, C:H.327, H2O.379 ZN.6: 4 residues within 4Å: Chain B: D.186, E.217, H.327 Ligands: ZN.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.186, B:E.217, B:E.217, B:H.327, H2O.234 ZN.7: 6 residues within 4Å: Chain B: H.72, D.186, D.187, E.216, D.239 Ligands: ZN.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.72, B:D.186, B:D.239, B:D.239, H2O.234 ZN.8: 4 residues within 4Å: Chain A: D.186, E.217, H.327 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:E.217, A:E.217, A:H.327, H2O.83 ZN.9: 6 residues within 4Å: Chain G: H.72, D.186, D.187, E.216, D.239 Ligands: ZN.13 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.72, G:D.186, G:D.239, G:D.239, H2O.1024 ZN.10: 6 residues within 4Å: Chain E: H.72, D.186, D.187, E.216, D.239 Ligands: ZN.16 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.72, E:D.186, E:D.239, E:D.239, H2O.728 ZN.11: 6 residues within 4Å: Chain H: H.72, D.186, D.187, E.216, D.239 Ligands: ZN.12 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.72, H:D.186, H:D.239, H:D.239, H2O.1177 ZN.12: 4 residues within 4Å: Chain H: D.186, E.217, H.327 Ligands: ZN.11 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.186, H:E.217, H:E.217, H:H.327, H2O.1177 ZN.13: 4 residues within 4Å: Chain G: D.186, E.217, H.327 Ligands: ZN.9 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.186, G:E.217, G:E.217, G:H.327, H2O.1024 ZN.14: 4 residues within 4Å: Chain F: D.186, E.217, H.327 Ligands: ZN.15 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.186, F:E.217, F:E.217, F:H.327, H2O.879 ZN.15: 6 residues within 4Å: Chain F: H.72, D.186, D.187, E.216, D.239 Ligands: ZN.14 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.72, F:D.186, F:D.239, F:D.239, H2O.879 ZN.16: 4 residues within 4Å: Chain E: D.186, E.217, H.327 Ligands: ZN.10 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.186, E:E.217, E:E.217, E:H.327, H2O.728 ZN.17: 6 residues within 4Å: Chain K: H.72, D.186, D.187, E.216, D.239 Ligands: ZN.21 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:H.72, K:D.186, K:D.239, K:D.239, H2O.1669 ZN.18: 6 residues within 4Å: Chain I: H.72, D.186, D.187, E.216, D.239 Ligands: ZN.24 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:H.72, I:D.186, I:D.239, I:D.239, H2O.1373 ZN.19: 6 residues within 4Å: Chain L: H.72, D.186, D.187, E.216, D.239 Ligands: ZN.20 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:H.72, L:D.186, L:D.239, L:D.239, H2O.1822 ZN.20: 4 residues within 4Å: Chain L: D.186, E.217, H.327 Ligands: ZN.19 5 PLIP interactions: 4 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:D.186, L:E.217, L:E.217, L:H.327, H2O.1822 ZN.21: 4 residues within 4Å: Chain K: D.186, E.217, H.327 Ligands: ZN.17 5 PLIP interactions: 4 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:D.186, K:E.217, K:E.217, K:H.327, H2O.1669 ZN.22: 4 residues within 4Å: Chain J: D.186, E.217, H.327 Ligands: ZN.23 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.186, J:E.217, J:E.217, J:H.327, H2O.1524 ZN.23: 6 residues within 4Å: Chain J: H.72, D.186, D.187, E.216, D.239 Ligands: ZN.22 5 PLIP interactions: 4 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:H.72, J:D.186, J:D.239, J:D.239, H2O.1524 ZN.24: 4 residues within 4Å: Chain I: D.186, E.217, H.327 Ligands: ZN.18 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.186, I:E.217, I:E.217, I:H.327, H2O.1373

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Russo, S. et al., Crystal structure of a dodecameric tetrahedral shaped aminopeptidase. J.Biol.Chem. (2004)

Release Date

2004-10-05

Peptides

Frv operon protein FrvX: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

Frv operon protein FrvX