SMTL ID : 9fxe.1

D204N mutant of Purine Nucleoside Phosphorylase from E.coli in complex with N2,3-etheno-2-aminopurine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: P.20, G.21, R.25, R.88, V.89, G.90, S.91 Chain B: R.44 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.21, A:V.89, A:S.91, A:S.91, A:R.218 Salt bridges: A:R.25, A:R.88, B:R.44 PO4.3: 7 residues within 4Å: Chain A: R.44 Chain B: P.20, G.21, R.88, V.89, G.90, S.91 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Salt bridges: A:R.44, B:R.88 Hydrogen bonds: B:G.21, B:S.91, B:S.91 Water bridges: B:D.22, B:D.22 PO4.5: 6 residues within 4Å: Chain C: G.21, R.88, V.89, G.90, S.91 Chain F: R.44 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:G.21, C:D.22, C:S.91, C:S.91, C:S.91 Water bridges: C:R.88 Salt bridges: C:R.88, F:R.44 PO4.7: 8 residues within 4Å: Chain D: P.20, G.21, R.25, R.88, V.89, G.90, S.91 Chain E: R.44 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:G.21, D:V.89, D:S.91, D:S.91, D:R.218 Salt bridges: D:R.25, D:R.88, E:R.44 PO4.9: 7 residues within 4Å: Chain D: R.44 Chain E: P.20, G.21, R.88, V.89, G.90, S.91 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:G.21, E:S.91, E:S.91 Water bridges: E:D.22, E:D.22 Salt bridges: E:R.88, D:R.44 PO4.11: 6 residues within 4Å: Chain C: R.44 Chain F: G.21, R.88, V.89, G.90, S.91 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:G.21, F:D.22, F:S.91, F:S.91, F:S.91 Water bridges: F:R.88 Salt bridges: F:R.88, C:R.44

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, N.205, I.207, R.218 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.91, A:N.205 Water bridges: A:F.160 01.4: 10 residues within 4Å: Chain B: S.91, C.92, G.93, F.160, V.179, E.180, M.181, S.204, N.205, I.207 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.91, B:G.93, B:N.205 01.6: 10 residues within 4Å: Chain C: S.91, C.92, G.93, F.160, V.179, E.180, M.181, S.204, N.205, I.207 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.91 01.8: 11 residues within 4Å: Chain D: S.91, C.92, G.93, F.160, V.179, E.180, M.181, S.204, N.205, I.207, R.218 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.91, D:N.205 Water bridges: D:F.160 01.10: 10 residues within 4Å: Chain E: S.91, C.92, G.93, F.160, V.179, E.180, M.181, S.204, N.205, I.207 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.91, E:G.93, E:N.205 01.12: 10 residues within 4Å: Chain F: S.91, C.92, G.93, F.160, V.179, E.180, M.181, S.204, N.205, I.207 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.91

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
C

C
B

D
A

E
C

F
B

Purine nucleoside phosphorylase DeoD-type