SMTL ID : 4da0.1

Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in complex with 2'-deoxyguanosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-hexamer

Ligands

6 x GNG: 2'-DEOXY-GUANOSINE(Non-covalent)

GNG.1: 14 residues within 4Å: Chain A: M.84, S.110, C.111, G.112, F.179, V.197, E.198, M.199, E.200, S.222, V.225 Chain E: H.24, R.63 Ligands: CL.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:E.198, A:M.199 Hydrogen bonds: A:S.222, E:H.24 GNG.3: 14 residues within 4Å: Chain B: M.84, S.110, C.111, G.112, F.179, V.197, E.198, M.199, E.200, S.222, V.225 Chain D: H.24, R.63 Ligands: CL.4 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:E.198, B:M.199 Hydrogen bonds: B:S.222, D:H.24 GNG.5: 14 residues within 4Å: Chain C: M.84, S.110, C.111, G.112, F.179, V.197, E.198, M.199, E.200, S.222, V.225 Chain F: H.24, R.63 Ligands: CL.6 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:E.198, C:M.199 Hydrogen bonds: C:S.222, F:H.24 GNG.7: 14 residues within 4Å: Chain B: H.24, R.63 Chain D: M.84, S.110, C.111, G.112, F.179, V.197, E.198, M.199, E.200, S.222, V.225 Ligands: CL.8 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:H.24, D:S.222 Hydrophobic interactions: D:E.198, D:M.199 GNG.9: 14 residues within 4Å: Chain A: H.24, R.63 Chain E: M.84, S.110, C.111, G.112, F.179, V.197, E.198, M.199, E.200, S.222, V.225 Ligands: CL.10 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:H.24, E:S.222 Hydrophobic interactions: E:E.198, E:M.199 GNG.11: 14 residues within 4Å: Chain C: H.24, R.63 Chain F: M.84, S.110, C.111, G.112, F.179, V.197, E.198, M.199, E.200, S.222, V.225 Ligands: CL.12 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain C Hydrophobic interactions: F:E.198, F:M.199 Hydrogen bonds: F:S.222, C:H.24

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

CL.2: 5 residues within 4Å: Chain A: G.40, R.107, G.109, S.110 Ligands: GNG.1 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain B: G.40, R.107, G.109, S.110 Ligands: GNG.3 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain C: G.40, R.107, G.109, S.110 Ligands: GNG.5 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain D: G.40, R.107, G.109, S.110 Ligands: GNG.7 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain E: G.40, R.107, G.109, S.110 Ligands: GNG.9 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain F: G.40, R.107, G.109, S.110 Ligands: GNG.11 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Giuseppe, P.O. et al., Insights into phosphate cooperativity and influence of substrate modifications on binding and catalysis of hexameric purine nucleoside phosphorylases. Plos One (2012)

Release Date

2012-09-26

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

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