SMTL ID : 5i3c.1

Crystal structure of E.coli purine nucleoside phosphorylase with acycloguanosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-hexamer

Ligands

6 x AC2: 9-HYROXYETHOXYMETHYLGUANINE(Non-covalent)

AC2.1: 13 residues within 4Å: Chain A: M.64, S.90, C.91, G.92, A.156, F.159, V.178, E.179, M.180, I.206 Chain E: H.4, R.43 Ligands: SO4.2 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:H.4, E:R.43, A:E.179 Water bridges: A:F.159 AC2.3: 12 residues within 4Å: Chain B: S.90, C.91, G.92, A.156, F.159, V.178, E.179, M.180, I.206 Chain D: H.4, R.43 Ligands: SO4.4 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:E.179, D:R.43 Water bridges: B:F.159 AC2.5: 14 residues within 4Å: Chain C: M.64, S.90, C.91, G.92, A.156, F.159, V.178, E.179, M.180, D.204, I.206 Chain F: H.4, R.43 Ligands: SO4.6 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain C Hydrogen bonds: F:H.4 Water bridges: C:F.159, C:F.159 AC2.9: 13 residues within 4Å: Chain B: H.4, R.43 Chain D: M.64, S.90, C.91, G.92, A.156, F.159, V.178, E.179, M.180, I.206 Ligands: SO4.10 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:H.4, B:R.43, D:E.179 Water bridges: D:F.159 AC2.11: 12 residues within 4Å: Chain A: H.4, R.43 Chain E: S.90, C.91, G.92, A.156, F.159, V.178, E.179, M.180, I.206 Ligands: SO4.12 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:E.179, A:R.43 Water bridges: E:F.159 AC2.13: 14 residues within 4Å: Chain C: H.4, R.43 Chain F: M.64, S.90, C.91, G.92, A.156, F.159, V.178, E.179, M.180, D.204, I.206 Ligands: SO4.14 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:D.204, C:H.4 Water bridges: F:F.159, F:F.159

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

SO4.2: 7 residues within 4Å: Chain A: P.19, G.20, R.87, G.89, S.90 Chain E: R.43 Ligands: AC2.1 7 PLIP interactions: 1 interactions with chain E, 6 interactions with chain A Salt bridges: E:R.43, A:R.87 Hydrogen bonds: A:G.20, A:S.90, A:S.90 Water bridges: A:D.21, A:D.21 SO4.4: 7 residues within 4Å: Chain B: P.19, G.20, R.87, G.89, S.90 Chain D: R.43 Ligands: AC2.3 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.20, B:S.90 Salt bridges: B:R.87, D:R.43 SO4.6: 8 residues within 4Å: Chain C: P.19, G.20, R.24, R.87, G.89, S.90 Chain F: R.43 Ligands: AC2.5 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:G.20, C:R.24, C:S.90, C:S.90 Water bridges: C:D.21, C:D.21 Salt bridges: C:R.87, F:R.43 SO4.7: 3 residues within 4Å: Chain C: Q.218, T.219, N.222 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.222 SO4.8: 3 residues within 4Å: Chain C: R.101, E.216, T.219 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.101 SO4.10: 7 residues within 4Å: Chain B: R.43 Chain D: P.19, G.20, R.87, G.89, S.90 Ligands: AC2.9 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.20, D:S.90, D:S.90 Water bridges: D:D.21, D:D.21 Salt bridges: D:R.87, B:R.43 SO4.12: 7 residues within 4Å: Chain A: R.43 Chain E: P.19, G.20, R.87, G.89, S.90 Ligands: AC2.11 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:G.20, E:S.90 Salt bridges: E:R.87, A:R.43 SO4.14: 8 residues within 4Å: Chain C: R.43 Chain F: P.19, G.20, R.24, R.87, G.89, S.90 Ligands: AC2.13 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain F Salt bridges: C:R.43, F:R.87 Hydrogen bonds: F:G.20, F:R.24, F:S.90, F:S.90 Water bridges: F:D.21, F:D.21 SO4.15: 3 residues within 4Å: Chain F: Q.218, T.219, N.222 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.222 SO4.16: 3 residues within 4Å: Chain F: R.101, E.216, T.219 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Timofeev, V.I. et al., Crystal structure of Escherichia coli purine nucleoside phosphorylase complexed with acyclovir. Acta Crystallogr F Struct Biol Commun (2018)

Release Date

2017-02-22

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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