SMTL ID : 1odi.1

Purine nucleoside phosphorylase from Thermus Thermophilus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 10 residues within 4Å: Chain A: P.20, G.21, D.22, R.25, R.87, G.89, T.90, E.181 Chain B: R.44 Ligands: ADN.2 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 SO4.3: 9 residues within 4Å: Chain A: R.44 Chain B: G.21, R.25, R.87, V.88, G.89, T.90, E.181 Ligands: ADN.4 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.21, B:T.90, B:T.90 Salt bridges: B:R.25, B:R.87, A:R.44 SO4.5: 10 residues within 4Å: Chain C: P.20, G.21, D.22, R.25, R.87, G.89, T.90, E.181 Chain D: R.44 Ligands: ADN.7 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.21, C:D.22, C:T.90 Salt bridges: C:R.25, C:R.87, D:R.44 SO4.6: 4 residues within 4Å: Chain B: R.135, R.139 Chain C: R.135, R.139 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Salt bridges: C:R.135, C:R.139, B:R.135, B:R.139 SO4.8: 10 residues within 4Å: Chain C: R.44 Chain D: G.21, D.22, R.25, R.87, V.88, G.89, T.90, E.181 Ligands: ADN.9 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 SO4.10: 11 residues within 4Å: Chain E: P.20, G.21, D.22, R.25, R.87, V.88, G.89, T.90, E.181 Chain F: R.44 Ligands: ADN.11 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 SO4.12: 11 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, E.181 Ligands: ADN.14 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 SO4.13: 3 residues within 4Å: Chain A: 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

6 x ADN: ADENOSINE(Non-covalent)

ADN.2: 17 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, N.204, I.206 Chain B: H.5, R.44 Ligands: SO4.1 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:H.5, B:R.44, A:R.87, A:M.180, A:E.181, A:N.204, A:N.204 Water bridges: A:G.207, A:G.207 ADN.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 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:H.5, A:R.44, B:R.87, B:M.180, B:E.181, B:N.204, B:N.204 ADN.7: 17 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, S.203, N.204, I.206 Chain D: H.5, R.44 Ligands: SO4.5 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.87, C:T.90, C:M.180, C:E.181, C:N.204, C:N.204, D:H.5, D:R.44 Water bridges: C:S.203 ADN.9: 17 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, I.206 Ligands: SO4.8 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.87, D:E.156, D:M.180, D:E.181, D:N.204, D:N.204, C:H.5, C:R.44 ADN.11: 17 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, I.206 Chain F: H.5, R.44 Ligands: SO4.10 11 PLIP interactions: 2 interactions with chain F, 9 interactions with chain E Hydrogen bonds: F:H.5, F:R.44, E:R.87, E:T.90, E:E.156, E:M.180, E:E.181, E:N.204, E:N.204 Water bridges: E:G.207, E:G.207 ADN.14: 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: SO4.12 9 PLIP interactions: 7 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:T.90, F:E.156, F:M.180, F:E.181, F:N.204, F:N.204, E:H.5, E:R.44 Water bridges: F:G.207

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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