SMTL ID : 3fow.1

Plasmodium Purine Nucleoside Phosphorylase V66I-V73I-Y160F Mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: G.25, D.26, R.29, R.90, G.92, S.93 Chain B: R.47 Ligands: IMH.4 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.25, A:D.26, A:R.90, A:R.90, A:S.93, A:S.93 Salt bridges: A:R.29, B:R.47 PO4.2: 2 residues within 4Å: Chain E: R.118 Chain F: R.171 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A, 2 interactions with chain E Salt bridges: F:R.171 Hydrogen bonds: A:G.126, E:R.118 Water bridges: E:R.118 PO4.3: 3 residues within 4Å: Chain A: R.171 Chain B: R.118 Chain F: D.127 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain F Salt bridges: A:R.171 Hydrogen bonds: F:G.126, F:D.127 PO4.5: 8 residues within 4Å: Chain A: R.47 Chain B: G.25, D.26, R.29, R.90, G.92, S.93 Ligands: IMH.6 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.25, B:D.26, B:R.90, B:R.90, B:S.93, B:S.93 Salt bridges: B:R.29, A:R.47 PO4.7: 8 residues within 4Å: Chain C: G.25, D.26, R.29, R.90, G.92, S.93 Chain D: R.47 Ligands: IMH.10 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.25, C:D.26, C:R.90, C:R.90, C:S.93, C:S.93 Salt bridges: C:R.29, D:R.47 PO4.8: 2 residues within 4Å: Chain A: R.118 Chain B: R.171 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Salt bridges: B:R.171 Hydrogen bonds: A:R.118, C:G.126 Water bridges: A:R.118 PO4.9: 3 residues within 4Å: Chain B: D.127 Chain C: R.171 Chain D: R.118 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Salt bridges: C:R.171 Hydrogen bonds: B:G.126, B:D.127 PO4.11: 8 residues within 4Å: Chain C: R.47 Chain D: G.25, D.26, R.29, R.90, G.92, S.93 Ligands: IMH.12 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.25, D:D.26, D:R.90, D:R.90, D:S.93, D:S.93 Salt bridges: D:R.29, C:R.47 PO4.13: 8 residues within 4Å: Chain E: G.25, D.26, R.29, R.90, G.92, S.93 Chain F: R.47 Ligands: IMH.16 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.25, E:D.26, E:R.90, E:R.90, E:S.93, E:S.93 Salt bridges: E:R.29, F:R.47 PO4.14: 2 residues within 4Å: Chain C: R.118 Chain D: R.171 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain E, 1 interactions with chain D Hydrogen bonds: C:R.118, E:G.126 Water bridges: C:R.118 Salt bridges: D:R.171 PO4.15: 3 residues within 4Å: Chain D: D.127 Chain E: R.171 Chain F: R.118 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:G.126, D:D.127 Salt bridges: E:R.171 PO4.17: 8 residues within 4Å: Chain E: R.47 Chain F: G.25, D.26, R.29, R.90, G.92, S.93 Ligands: IMH.18 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.25, F:D.26, F:R.90, F:R.90, F:S.93, F:S.93 Salt bridges: F:R.29, E:R.47

6 x IMH: 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL(Non-covalent)

IMH.4: 14 residues within 4Å: Chain A: I.68, R.90, S.93, C.94, G.95, F.162, V.183, E.184, M.185, E.186, D.208, P.211 Chain B: H.9 Ligands: PO4.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:M.185, A:E.186, A:D.208, B:H.9 IMH.6: 14 residues within 4Å: Chain A: H.9 Chain B: I.68, R.90, S.93, C.94, G.95, F.162, V.183, E.184, M.185, E.186, D.208, P.211 Ligands: PO4.5 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.185, B:E.186, B:D.208, A:H.9 pi-Stacking: B:F.162 IMH.10: 14 residues within 4Å: Chain C: I.68, R.90, S.93, C.94, G.95, F.162, V.183, E.184, M.185, E.186, D.208, P.211 Chain D: H.9 Ligands: PO4.7 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:H.9, C:M.185, C:E.186, C:D.208 IMH.12: 14 residues within 4Å: Chain C: H.9 Chain D: I.68, R.90, S.93, C.94, G.95, F.162, V.183, E.184, M.185, E.186, D.208, P.211 Ligands: PO4.11 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:M.185, D:E.186, D:D.208, C:H.9 pi-Stacking: D:F.162 IMH.16: 14 residues within 4Å: Chain E: I.68, R.90, S.93, C.94, G.95, F.162, V.183, E.184, M.185, E.186, D.208, P.211 Chain F: H.9 Ligands: PO4.13 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:M.185, E:E.186, E:D.208, F:H.9 IMH.18: 14 residues within 4Å: Chain E: H.9 Chain F: I.68, R.90, S.93, C.94, G.95, F.162, V.183, E.184, M.185, E.186, D.208, P.211 Ligands: PO4.17 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:H.9, F:M.185, F:E.186, F:D.208 pi-Stacking: F:F.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Donaldson, T.M. et al., Structural determinants of the 5'-methylthioinosine specificity of Plasmodium purine nucleoside phosphorylase. Plos One (2014)

Release Date

2009-12-29

Peptides

Uridine phosphorylase, putative: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Uridine phosphorylase, putative