SMTL ID : 9fpe.1

Wild type Purine Nucleoside Phosphorylase from E.coli in complex with N2,3-etheno-2-aminopurine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-hexamer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: M.65, S.91, F.160, M.181, E.182 Chain C: H.5, R.44 Ligands: 01.2, PO4.3 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:H.5, C:R.44, A:E.182 Water bridges: A:S.91 GOL.6: 8 residues within 4Å: Chain B: M.65, S.91, F.160, M.181, E.182 Chain E: H.5, R.44 Ligands: PO4.5 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:E.182, E:H.5, E:R.44 Water bridges: B:R.88, B:M.181 GOL.10: 9 residues within 4Å: Chain A: H.5, R.44 Chain C: M.65, S.91, F.160, M.181, E.182 Ligands: PO4.9, 01.11 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:H.5, A:R.44, C:S.91, C:E.182 Water bridges: C:S.91 GOL.13: 9 residues within 4Å: Chain D: M.65, S.91, F.160, M.181, E.182 Chain F: H.5, R.44 Ligands: 01.14, PO4.15 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:E.182, F:H.5, F:R.44 Water bridges: D:S.91 GOL.18: 8 residues within 4Å: Chain B: H.5, R.44 Chain E: M.65, S.91, F.160, M.181, E.182 Ligands: PO4.17 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:E.182, B:H.5, B:R.44 Water bridges: E:R.88, E:M.181 GOL.22: 9 residues within 4Å: Chain D: H.5, R.44 Chain F: M.65, S.91, F.160, M.181, E.182 Ligands: PO4.21, 01.23 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:S.91, F:E.182, D:H.5, D:R.44 Water bridges: F:S.91

6 x 01: N,2,3-etheno-2-aminopurine

01.2: 11 residues within 4Å: Chain A: S.91, C.92, G.93, F.160, V.179, E.180, M.181, S.204, D.205, I.207 Ligands: GOL.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.160 01.7: 10 residues within 4Å: Chain B: S.91, C.92, G.93, F.160, V.179, E.180, M.181, S.204, D.205, I.207 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.92 Water bridges: B:F.160 01.11: 11 residues within 4Å: Chain C: S.91, C.92, G.93, F.160, V.179, E.180, M.181, S.204, D.205, I.207 Ligands: GOL.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:C.92 Water bridges: C:F.160 01.14: 11 residues within 4Å: Chain D: S.91, C.92, G.93, F.160, V.179, E.180, M.181, S.204, D.205, I.207 Ligands: GOL.13 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:F.160 01.19: 10 residues within 4Å: Chain E: S.91, C.92, G.93, F.160, V.179, E.180, M.181, S.204, D.205, I.207 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:C.92 Water bridges: E:F.160 01.23: 11 residues within 4Å: Chain F: S.91, C.92, G.93, F.160, V.179, E.180, M.181, S.204, D.205, I.207 Ligands: GOL.22 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:C.92 Water bridges: F:F.160

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 9 residues within 4Å: Chain A: P.20, G.21, R.25, R.88, V.89, G.90, S.91 Chain C: R.44 Ligands: GOL.1 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.21, A:V.89, A:S.91, A:S.91 Water bridges: A:S.91 Salt bridges: A:R.25, A:R.88, C:R.44 PO4.5: 7 residues within 4Å: Chain B: G.21, R.88, V.89, G.90, S.91 Chain E: R.44 Ligands: GOL.6 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:G.21, B:D.22, B:S.91, B:S.91, B:S.91 Water bridges: B:R.88, B:V.89 Salt bridges: B:R.88, E:R.44 PO4.9: 8 residues within 4Å: Chain A: R.44 Chain C: P.20, G.21, R.88, V.89, G.90, S.91 Ligands: GOL.10 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain C Salt bridges: A:R.44, C:R.88 Hydrogen bonds: C:G.21, C:S.91, C:S.91 Water bridges: C:D.22, C:D.22 PO4.15: 9 residues within 4Å: Chain D: P.20, G.21, R.25, R.88, V.89, G.90, S.91 Chain F: R.44 Ligands: GOL.13 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:G.21, D:V.89, D:S.91, D:S.91 Water bridges: D:S.91 Salt bridges: D:R.25, D:R.88, F:R.44 PO4.17: 7 residues within 4Å: Chain B: R.44 Chain E: G.21, R.88, V.89, G.90, S.91 Ligands: GOL.18 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain E Salt bridges: B:R.44, E:R.88 Hydrogen bonds: E:G.21, E:D.22, E:S.91, E:S.91, E:S.91 Water bridges: E:R.88, E:V.89 PO4.21: 8 residues within 4Å: Chain D: R.44 Chain F: P.20, G.21, R.88, V.89, G.90, S.91 Ligands: GOL.22 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain F Salt bridges: D:R.44, F:R.88 Hydrogen bonds: F:G.21, F:S.91, F:S.91 Water bridges: F:D.22, F:D.22

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

SO4.4: 3 residues within 4Å: Chain A: T.221, N.223, D.224 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.221, A:N.223 Water bridges: A:N.223, A:D.224 Salt bridges: A:K.227 SO4.8: 2 residues within 4Å: Chain B: T.220, N.223 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.220, B:N.223 Water bridges: B:Q.219, B:T.220 SO4.12: 3 residues within 4Å: Chain C: A.215, R.218, Q.219 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.219 Salt bridges: C:R.218 SO4.16: 3 residues within 4Å: Chain D: T.221, N.223, D.224 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.221, D:N.223 Water bridges: D:N.223, D:D.224 Salt bridges: D:K.227 SO4.20: 2 residues within 4Å: Chain E: T.220, N.223 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.220, E:N.223 Water bridges: E:Q.219, E:T.220 SO4.24: 3 residues within 4Å: Chain F: A.215, R.218, Q.219 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.219 Salt bridges: F:R.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stachelska-Wierzchowska, A. et al., Interaction of Tri-Cyclic Nucleobase Analogs with Enzymes of Purine Metabolism: Xanthine Oxidase and Purine Nucleoside Phosphorylase. Int J Mol Sci (2024)

Release Date

2024-10-30

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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