SMTL ID : 1yr3.1

Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-hexamer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 8 residues within 4Å: Chain A: G.33, S.34, H.65, R.85, H.87, N.116, A.117, S.216 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.34, A:N.116, A:A.117, A:S.216 Salt bridges: A:H.65, A:R.85, A:H.87 SO4.3: 8 residues within 4Å: Chain B: G.33, S.34, H.65, R.85, H.87, N.116, A.117, S.216 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.34, B:N.116, B:A.117, B:S.216 Salt bridges: B:H.65, B:R.85, B:H.87 SO4.5: 8 residues within 4Å: Chain C: G.33, S.34, H.65, R.85, H.87, N.116, A.117, S.216 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.34, C:N.116, C:A.117, C:S.216 Salt bridges: C:H.65, C:R.85, C:H.87 SO4.7: 8 residues within 4Å: Chain D: G.33, S.34, H.65, R.85, H.87, N.116, A.117, S.216 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.34, D:N.116, D:A.117, D:S.216 Salt bridges: D:H.65, D:R.85, D:H.87 SO4.9: 8 residues within 4Å: Chain E: G.33, S.34, H.65, R.85, H.87, N.116, A.117, S.216 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:S.34, E:N.116, E:A.117, E:S.216 Salt bridges: E:H.65, E:R.85, E:H.87 SO4.11: 8 residues within 4Å: Chain F: G.33, S.34, H.65, R.85, H.87, N.116, A.117, S.216 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:S.34, F:N.116, F:A.117, F:S.216 Salt bridges: F:H.65, F:R.85, F:H.87

6 x XAN: XANTHINE(Non-covalent)

XAN.2: 12 residues within 4Å: Chain A: A.117, A.118, G.119, F.196, E.197, V.213, G.214, M.215, T.238, N.239, L.249, T.254 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.117, A:E.197, A:M.215, A:N.239 pi-Stacking: A:F.196 XAN.4: 12 residues within 4Å: Chain B: A.117, A.118, G.119, F.196, E.197, V.213, G.214, M.215, T.238, N.239, L.249, T.254 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.117, B:E.197, B:M.215, B:N.239 pi-Stacking: B:F.196 XAN.6: 12 residues within 4Å: Chain C: A.117, A.118, G.119, F.196, E.197, V.213, G.214, M.215, T.238, N.239, L.249, T.254 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.117, C:E.197, C:M.215, C:N.239 pi-Stacking: C:F.196 XAN.8: 12 residues within 4Å: Chain D: A.117, A.118, G.119, F.196, E.197, V.213, G.214, M.215, T.238, N.239, L.249, T.254 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:A.117, D:E.197, D:M.215, D:N.239 pi-Stacking: D:F.196 XAN.10: 12 residues within 4Å: Chain E: A.117, A.118, G.119, F.196, E.197, V.213, G.214, M.215, T.238, N.239, L.249, T.254 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:A.117, E:E.197, E:M.215, E:N.239 pi-Stacking: E:F.196 XAN.12: 12 residues within 4Å: Chain F: A.117, A.118, G.119, F.196, E.197, V.213, G.214, M.215, T.238, N.239, L.249, T.254 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:A.117, F:E.197, F:M.215, F:N.239 pi-Stacking: F:F.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dandanell, G. et al., Escherichia coli purine nucleoside phosphorylase II, the product of the xapA gene. J.Mol.Biol. (2005)

Release Date

2005-04-19

Peptides

Xanthosine phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Xanthosine phosphorylase

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