SMTL ID : 1gyt.1 (1 other biounit)

E. coli Aminopeptidase A (PepA)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: K.270, D.275, D.293, E.354 Ligands: ZN.2, CO3.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.275, A:D.293, A:E.354, H2O.3 ZN.2: 4 residues within 4Å: Chain A: D.275, D.352, E.354 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.275, A:D.352, A:D.352, A:E.354, H2O.3 ZN.4: 6 residues within 4Å: Chain B: K.270, D.275, D.293, E.354 Ligands: ZN.5, CO3.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.275, B:D.293, B:E.354, H2O.16 ZN.5: 4 residues within 4Å: Chain B: D.275, D.352, E.354 Ligands: ZN.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.275, B:D.352, B:D.352, B:E.354, H2O.16 ZN.8: 6 residues within 4Å: Chain C: K.270, D.275, D.293, E.354 Ligands: ZN.9, CO3.10 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.275, C:D.293, C:E.354, H2O.26 ZN.9: 4 residues within 4Å: Chain C: D.275, D.352, E.354 Ligands: ZN.8 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.275, C:D.352, C:D.352, C:E.354, H2O.26 ZN.11: 6 residues within 4Å: Chain D: K.270, D.275, D.293, E.354 Ligands: ZN.12, CO3.13 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.275, D:D.293, D:E.354, H2O.41 ZN.12: 4 residues within 4Å: Chain D: D.275, D.352, E.354 Ligands: ZN.11 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.275, D:D.352, D:D.352, D:E.354, H2O.41 ZN.14: 6 residues within 4Å: Chain E: K.270, D.275, D.293, E.354 Ligands: ZN.15, CO3.16 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.275, E:D.293, E:D.293, E:E.354, H2O.51 ZN.15: 4 residues within 4Å: Chain E: D.275, D.352, E.354 Ligands: ZN.14 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.275, E:D.352, E:D.352, E:E.354, H2O.51 ZN.17: 6 residues within 4Å: Chain F: K.270, D.275, D.293, E.354 Ligands: ZN.18, CO3.19 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.275, F:D.293, F:D.293, F:E.354, H2O.67 ZN.18: 4 residues within 4Å: Chain F: D.275, D.352, E.354 Ligands: ZN.17 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.275, F:D.352, F:D.352, F:E.354, H2O.67

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

CO3.3: 8 residues within 4Å: Chain A: K.270, D.352, A.353, E.354, G.355, R.356, L.380 Ligands: ZN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.354, A:R.356, A:R.356, A:R.356 CO3.6: 8 residues within 4Å: Chain B: K.270, D.352, A.353, E.354, G.355, R.356, L.380 Ligands: ZN.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.354, B:R.356, B:R.356, B:R.356 CO3.10: 8 residues within 4Å: Chain C: K.270, D.352, A.353, E.354, G.355, R.356, L.380 Ligands: ZN.8 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.354, C:G.355, C:R.356, C:R.356, C:R.356 CO3.13: 8 residues within 4Å: Chain D: K.270, D.352, A.353, E.354, G.355, R.356, L.380 Ligands: ZN.11 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.354, D:R.356, D:R.356, D:R.356 CO3.16: 9 residues within 4Å: Chain E: K.270, D.352, A.353, E.354, G.355, R.356, L.380, T.381 Ligands: ZN.14 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:E.354, E:G.355, E:R.356, E:R.356, E:R.356 CO3.19: 8 residues within 4Å: Chain F: K.270, D.352, A.353, E.354, G.355, R.356, L.380 Ligands: ZN.17 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:E.354, F:G.355, F:R.356, F:R.356, F:R.356

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 4 residues within 4Å: Chain A: G.329 Chain B: G.329, R.330 Chain C: G.329 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain D: G.329, R.330 Chain E: G.329 Chain F: G.329, R.330 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Straeter, N. et al., X-Ray Structure of Aminopeptidase a from Escherichia Coli and a Model for the Nucleoprotein Complex in Xer Site-Specific Recombination. Embo J. (1999)

Release Date

2002-06-06

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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