SMTL ID : 1odl.1

PURINE NUCLEOSIDE PHOSPHORYLASE FROM THERMUS THERMOPHILUS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 9 residues within 4Å: Chain A: P.20, G.21, D.22, R.25, R.87, V.88, G.89, T.90 Chain B: R.44 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.21, A:D.22, A:T.90, A:T.90 Salt bridges: A:R.25, A:R.87, B:R.44 SO4.2: 4 residues within 4Å: Chain A: R.135, R.139 Chain F: R.135, R.139 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain F Salt bridges: A:R.135, A:R.139, F:R.135, F:R.139 SO4.6: 7 residues within 4Å: Chain A: R.44 Chain B: G.21, R.25, R.87, V.88, G.89, T.90 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.21, B:T.90 Water bridges: B:T.90, B:T.90, B:T.90, B:E.181, B:E.181 Salt bridges: B:R.25, B:R.87, A:R.44 SO4.7: 4 residues within 4Å: Chain B: R.135, R.139 Chain C: R.135, R.139 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Water bridges: C:R.135, C:R.135 Salt bridges: C:R.135, C:R.139, B:R.135 SO4.11: 9 residues within 4Å: Chain C: P.20, G.21, D.22, R.25, R.87, V.88, G.89, T.90 Chain D: R.44 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.21, C:D.22, C:T.90, C:T.90 Salt bridges: C:R.25, C:R.87, D:R.44 SO4.13: 7 residues within 4Å: Chain C: R.44 Chain D: G.21, D.22, R.25, R.87, G.89, T.90 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.21, D:D.22, D:T.90, D:T.90 Salt bridges: D:R.25, D:R.87, C:R.44 SO4.16: 8 residues within 4Å: Chain E: G.21, D.22, R.25, R.87, V.88, G.89, T.90 Chain F: R.44 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.21, E:D.22, E:T.90, E:T.90 Salt bridges: E:R.25, E:R.87, F:R.44 SO4.19: 9 residues within 4Å: Chain E: R.44 Chain F: P.20, G.21, D.22, R.25, R.87, V.88, G.89, T.90 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.21, F:D.22, F:T.90, F:T.90 Salt bridges: F:R.25, F:R.87, E:R.44

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: A.169, W.170, Y.173 Chain F: L.120, E.121, R.123 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:R.123, A:Y.173 GOL.4: 4 residues within 4Å: Chain A: R.123 Chain F: A.169, W.170, Y.173 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:E.121, A:R.123, F:Y.173 GOL.8: 6 residues within 4Å: Chain B: E.166, A.169, W.170, Y.173 Chain C: L.120, R.123 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.123, B:E.166, B:Y.173 GOL.9: 6 residues within 4Å: Chain B: L.120, E.121, R.123 Chain C: A.169, W.170, Y.173 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.121 Water bridges: B:R.123, B:R.123 GOL.14: 7 residues within 4Å: Chain D: A.169, W.170, Y.173 Chain E: Y.119, L.120, E.121, R.123 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:W.170, D:Y.173, E:E.121, E:R.123, E:R.123 GOL.17: 6 residues within 4Å: Chain D: L.120, E.121, R.123 Chain E: A.169, W.170, Y.173 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:E.121, D:R.123, D:R.123, E:Y.173

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

CL.5: 3 residues within 4Å: Chain A: A.14, E.15, P.57 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: A.14, E.15, P.57 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain C: A.14, E.15, P.57 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain D: A.14, E.15, P.57 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain E: A.14, E.15, P.57 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain F: A.14, E.15, P.57 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tahirov, T.H. et al., Crystal Structure of Purine Nucleoside Phosphorylase from Thermus Thermophilus. J.Mol.Biol. (2004)

Release Date

2003-02-27

Peptides

PURINE NUCLEOSIDE PHOSPHORYLASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

PURINE NUCLEOSIDE PHOSPHORYLASE

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