SMTL ID : 1odj.1

PURINE NUCLEOSIDE PHOSPHORYLASE FROM THERMUS THERMOPHILUS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

6 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, G.89, T.90 Chain B: R.44 Ligands: GMP.2 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.21, A:D.22, A:T.90 Salt bridges: A:R.25, A:R.87, B:R.44 SO4.3: 10 residues within 4Å: Chain A: R.44 Chain B: G.21, D.22, R.25, R.87, V.88, G.89, T.90, E.181 Ligands: GMP.4 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.21, B:D.22, B:T.90 Salt bridges: B:R.25, B:R.87, A:R.44 SO4.5: 8 residues within 4Å: Chain C: G.21, R.25, R.87, V.88, G.89, T.90 Chain D: R.44 Ligands: GMP.6 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 SO4.7: 9 residues within 4Å: Chain C: R.44 Chain D: P.20, G.21, R.25, R.87, G.89, T.90, E.181 Ligands: GMP.8 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.21, D:T.90 Salt bridges: D:R.25, D:R.87, C:R.44 SO4.9: 10 residues within 4Å: Chain E: P.20, G.21, D.22, R.25, R.87, G.89, T.90, E.181 Chain F: R.44 Ligands: GMP.10 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 SO4.11: 8 residues within 4Å: Chain E: R.44 Chain F: G.21, R.25, R.87, G.89, T.90, E.181 Ligands: GMP.12 6 PLIP interactions: 1 interactions with chain E, 5 interactions with chain F Salt bridges: E:R.44, F:R.25, F:R.87 Hydrogen bonds: F:G.21, F:T.90, F:T.90

6 x GMP: GUANOSINE(Non-covalent)

GMP.2: 16 residues within 4Å: Chain A: M.65, R.87, T.90, A.91, G.92, E.156, F.159, F.178, E.179, M.180, E.181, S.203, I.206 Chain B: H.5, R.44 Ligands: SO4.1 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.87, A:E.179, A:M.180, A:E.181, A:N.204, B:H.5, B:R.44 Water bridges: A:F.159 Salt bridges: A:E.156 GMP.4: 17 residues within 4Å: Chain A: H.5, R.44 Chain B: M.65, R.87, T.90, A.91, G.92, E.156, F.159, F.178, E.179, M.180, E.181, S.203, N.204, I.206 Ligands: SO4.3 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.87, B:E.179, B:M.180, B:E.181, B:N.204, A:H.5, A:R.44 Salt bridges: B:E.156 GMP.6: 15 residues within 4Å: Chain C: M.65, R.87, T.90, A.91, G.92, E.156, F.159, F.178, E.179, M.180, E.181, N.204 Chain D: H.5, R.44 Ligands: SO4.5 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.87, C:T.90, C:E.179, C:E.179, C:M.180, C:E.181, D:H.5 Salt bridges: C:E.156 pi-Stacking: C:F.159 GMP.8: 16 residues within 4Å: Chain C: H.5, R.44 Chain D: M.65, R.87, T.90, A.91, G.92, E.156, F.159, F.178, E.179, M.180, E.181, S.203, N.204 Ligands: SO4.7 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:H.5, C:R.44, D:R.87, D:E.179, D:M.180, D:E.181, D:N.204 Salt bridges: D:E.156 GMP.10: 16 residues within 4Å: Chain E: M.65, R.87, T.90, A.91, G.92, E.156, F.159, F.178, E.179, M.180, E.181, S.203, N.204 Chain F: H.5, R.44 Ligands: SO4.9 10 PLIP interactions: 2 interactions with chain F, 8 interactions with chain E Hydrogen bonds: F:H.5, F:R.44, E:R.87, E:T.90, E:E.179, E:M.180, E:E.181, E:S.203, E:N.204 Salt bridges: E:E.156 GMP.12: 17 residues within 4Å: Chain E: H.5, R.44 Chain F: M.65, R.87, T.90, A.91, G.92, E.156, F.159, F.178, E.179, M.180, E.181, S.203, N.204, I.206 Ligands: SO4.11 13 PLIP interactions: 11 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:R.87, F:T.90, F:G.92, F:E.179, F:M.180, F:E.181, F:S.203, F:N.204, E:H.5, E:R.44 Water bridges: F:E.156 Salt bridges: F:E.156 pi-Stacking: F:F.159

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

2003-03-04

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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