SMTL ID : 1nw4.5 (6 other biounits)

Crystal Structure of Plasmodium falciparum Purine Nucleoside Phosphorylase in complex with ImmH and Sulfate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: G.25, R.90, G.92, S.93 Chain B: R.47 Ligands: IMH.4 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Salt bridges: B:R.47, A:R.90 Hydrogen bonds: A:G.25, A:S.93 Water bridges: A:D.26, A:D.26 SO4.2: 4 residues within 4Å: Chain A: H.125, G.126, D.127 Ligands: IPA.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.126, A:D.127 Water bridges: A:D.127, A:D.127 SO4.3: 3 residues within 4Å: Chain A: K.103, R.104, D.218 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.104, A:D.218 Salt bridges: A:K.103, A:R.104 SO4.7: 7 residues within 4Å: Chain A: R.47 Chain B: G.25, R.90, A.91, G.92, S.93 Ligands: IMH.11 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.25, B:A.91, B:S.93 Salt bridges: B:R.90, A:R.47 SO4.8: 4 residues within 4Å: Chain B: H.125, G.126, D.127 Ligands: IPA.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.126, B:D.127 SO4.9: 3 residues within 4Å: Chain B: K.103, R.104, D.218 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.104, B:D.218 Salt bridges: B:K.103, B:R.104 SO4.10: 5 residues within 4Å: Chain B: R.29, N.221, N.222, L.223, L.228 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.221, B:L.223 Salt bridges: B:R.29, B:K.32

2 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: R.90, S.93, C.94, G.95, Y.162, V.183, E.184, M.185, E.186, D.208, W.214 Chain B: H.9 Ligands: SO4.1, IPA.12 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:H.9, A:M.185, A:E.186, A:D.208 Water bridges: B:R.47, A:Y.162, A:Y.162, A:D.208 pi-Stacking: A:Y.162 IMH.11: 16 residues within 4Å: Chain A: H.9, R.47 Chain B: V.68, R.90, S.93, C.94, G.95, Y.162, V.183, E.184, M.185, E.186, D.208, W.214 Ligands: IPA.5, SO4.7 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:M.185, B:E.186, B:D.208, A:H.9, A:R.47 Water bridges: B:D.208

5 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.5: 6 residues within 4Å: Chain A: R.8, H.9, N.46, R.47 Chain B: F.219 Ligands: IMH.11 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.219 Water bridges: B:D.208 Hydrogen bonds: A:R.47 IPA.6: 3 residues within 4Å: Chain A: H.121, H.125 Ligands: SO4.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.125 IPA.12: 5 residues within 4Å: Chain A: F.219 Chain B: R.8, N.46, R.47 Ligands: IMH.4 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.47 Hydrophobic interactions: A:F.219 Water bridges: A:D.208, A:D.208, A:N.221 IPA.13: 4 residues within 4Å: Chain A: R.171 Chain B: R.118, H.121, L.122 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:H.121, B:L.122 Hydrogen bonds: B:R.118 IPA.14: 3 residues within 4Å: Chain B: H.121, H.125 Ligands: SO4.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, W. et al., Plasmodium falciparum Purine Nucleoside Phosphorylase: CRYSTAL STRUCTURES, IMMUCILLIN INHIBITORS, AND DUAL CATALYTIC FUNCTION. J.Biol.Chem. (2004)

Release Date

2004-03-16

Peptides

uridine phosphorylase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

uridine phosphorylase, putative

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