SMTL ID : 4ldn.1

Crystal structure of a putative purine nucleoside phosphorylase from Vibrio fischeri ES114 (Target NYSGRC-029521)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-hexamer

Ligands

12 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: P.42, G.43, R.110, I.111, G.112, S.113 Chain D: R.66 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.43, A:S.113 Water bridges: A:E.202, A:E.204 Salt bridges: A:R.110, D:R.66 PO4.2: 2 residues within 4Å: Chain A: H.232, H.234 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.232, A:H.234 PO4.8: 7 residues within 4Å: Chain B: P.42, G.43, R.110, I.111, G.112, S.113 Chain F: R.66 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:G.43, B:S.113 Water bridges: B:E.202, B:E.204 Salt bridges: B:R.110, F:R.66 PO4.9: 2 residues within 4Å: Chain B: H.232, H.234 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.232, B:H.234 PO4.15: 7 residues within 4Å: Chain C: P.42, G.43, R.110, I.111, G.112, S.113 Chain E: R.66 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:G.43, C:S.113 Water bridges: C:E.202, C:E.204 Salt bridges: C:R.110, E:R.66 PO4.16: 2 residues within 4Å: Chain C: H.232, H.234 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:H.232, C:H.234 PO4.22: 7 residues within 4Å: Chain A: R.66 Chain D: P.42, G.43, R.110, I.111, G.112, S.113 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.43, D:S.113 Water bridges: D:E.204, D:E.204 Salt bridges: D:R.110, A:R.66 PO4.23: 2 residues within 4Å: Chain D: H.232, H.234 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:H.232, D:H.234 PO4.29: 7 residues within 4Å: Chain C: R.66 Chain E: P.42, G.43, R.110, I.111, G.112, S.113 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:G.43, E:S.113 Water bridges: E:E.204, E:E.204 Salt bridges: E:R.110, C:R.66 PO4.30: 2 residues within 4Å: Chain E: H.232, H.234 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:H.232, E:H.234 PO4.36: 7 residues within 4Å: Chain B: R.66 Chain F: P.42, G.43, R.110, I.111, G.112, S.113 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:G.43, F:S.113 Water bridges: F:E.204, F:E.204 Salt bridges: F:R.110, B:R.66 PO4.37: 2 residues within 4Å: Chain F: H.232, H.234 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:H.232, F:H.234

30 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: N.139, R.142, F.148, S.210 Chain E: Y.196 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: Y.55, H.245, N.249 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: H.118, V.121, A.194, I.198, L.199 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: P.45, R.66, M.68 Chain D: R.66, M.68 Ligands: EDO.27 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: T.163, T.167, N.249, D.253 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain B: N.139, R.142, F.148, S.210 Chain D: Y.196 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain B: Y.55, H.245, N.249 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain B: H.118, V.121, A.194, I.198, L.199 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain B: P.45, R.66, M.68 Chain F: R.66, M.68 Ligands: EDO.41 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: T.163, T.167, N.249, D.253 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain C: N.139, R.142, F.148, S.210 Chain F: Y.196 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain C: Y.55, H.245, N.249 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain C: H.118, V.121, A.194, I.198, L.199 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain C: P.45, R.66, M.68 Chain E: R.66, M.68 Ligands: EDO.34 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain C: T.163, T.167, N.249, D.253 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: Y.196 Chain D: N.139, R.142, F.148, S.210 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain D: Y.55, H.245, N.249 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain D: H.118, V.121, A.194, I.198, L.199 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain A: R.66, M.68 Chain D: P.45, R.66, M.68 Ligands: EDO.6 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain D: T.163, T.167, N.249, D.253 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain A: Y.196 Chain E: N.139, R.142, F.148, S.210 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain E: Y.55, H.245, N.249 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain E: H.118, V.121, A.194, I.198, L.199 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain C: R.66, M.68 Chain E: P.45, R.66, M.68 Ligands: EDO.20 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain E: T.163, T.167, N.249, D.253 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain C: Y.196 Chain F: N.139, R.142, F.148, S.210 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain F: Y.55, H.245, N.249 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain F: H.118, V.121, A.194, I.198, L.199 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain B: R.66, M.68 Chain F: P.45, R.66, M.68 Ligands: EDO.13 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain F: T.163, T.167, N.249, D.253 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sampathkumar, P. et al., Crystal structure of a putative purine nucleoside phosphorylase from Vibrio fischeri ES114 (Target NYSGRC-029521). to be published

Release Date

2013-07-03

Peptides

Purine nucleoside phosphorylase DeoD-type: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Purine nucleoside phosphorylase DeoD-type