SMTL ID : 5iu6.1

Crystal structure of E.coli purine nucleoside phosphorylase with 7-deazahypoxanthine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-hexamer

Ligands

6 x 7HX: 7H-pyrrolo[2,3-d]pyrimidin-4-ol(Non-covalent)

7HX.1: 9 residues within 4Å: Chain A: S.90, C.91, G.92, F.159, V.178, E.179, M.180, S.203, D.204 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.159 Hydrogen bonds: A:G.92, A:D.204 7HX.3: 9 residues within 4Å: Chain B: S.90, C.91, G.92, A.156, F.159, V.178, E.179, M.180, I.206 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.159 Hydrogen bonds: B:G.92 7HX.5: 8 residues within 4Å: Chain C: S.90, C.91, G.92, F.159, V.178, E.179, M.180, D.204 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.159 Hydrogen bonds: C:G.92 7HX.7: 9 residues within 4Å: Chain D: S.90, C.91, G.92, F.159, V.178, E.179, M.180, S.203, D.204 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.159 Hydrogen bonds: D:G.92, D:D.204, D:D.204 7HX.9: 9 residues within 4Å: Chain E: S.90, C.91, G.92, A.156, F.159, V.178, E.179, M.180, I.206 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.159 Hydrogen bonds: E:G.92 7HX.11: 8 residues within 4Å: Chain F: S.90, C.91, G.92, F.159, V.178, E.179, M.180, D.204 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:F.159 Hydrogen bonds: F:G.92

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

SO4.2: 8 residues within 4Å: Chain A: P.19, G.20, R.24, R.87, V.88, G.89, S.90 Chain D: R.43 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain A Salt bridges: D:R.43, A:R.24, A:R.87 Hydrogen bonds: A:G.20, A:S.90, A:S.90 SO4.4: 6 residues within 4Å: Chain B: P.19, G.20, R.87, G.89, S.90 Chain F: R.43 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain F Hydrogen bonds: B:G.20, B:S.90, B:S.90 Water bridges: B:D.21, F:R.43, F:R.43 Salt bridges: B:R.87, F:R.43 SO4.6: 6 residues within 4Å: Chain C: P.19, G.20, R.87, G.89, S.90 Chain E: R.43 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:G.20, C:S.90 Water bridges: C:E.181, C:E.181 Salt bridges: C:R.87, E:R.43 SO4.8: 8 residues within 4Å: Chain A: R.43 Chain D: P.19, G.20, R.24, R.87, V.88, G.89, S.90 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.20, D:S.90, D:S.90 Salt bridges: D:R.24, D:R.87, A:R.43 SO4.10: 6 residues within 4Å: Chain C: R.43 Chain E: P.19, G.20, R.87, G.89, S.90 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain E Water bridges: C:R.43, C:R.43, E:D.21 Salt bridges: C:R.43, E:R.87 Hydrogen bonds: E:G.20, E:S.90, E:S.90 SO4.12: 6 residues within 4Å: Chain B: R.43 Chain F: P.19, G.20, R.87, G.89, S.90 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:G.20, F:S.90 Water bridges: F:E.181, F:E.181 Salt bridges: F:R.87, B:R.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Timofeev, V.I. et al., Crystal structure of Escherichia coli purine nucleoside phosphorylase in complex with 7-deazahypoxanthine. Acta Crystallogr F Struct Biol Commun (2018)

Release Date

2017-04-05

Peptides

Purine nucleoside phosphorylase DeoD-type: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Purine nucleoside phosphorylase DeoD-type

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