SMTL ID : 1q1g.1

Crystal structure of Plasmodium falciparum PNP with 5'-methylthio-immucillin-H

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: V.24, G.25, R.90, A.91, G.92, S.93 Chain B: R.47 Ligands: MTI.5 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: K.103, R.104, D.218 Ligand excluded by PLIP SO4.3: 5 residues within 4Å: Chain A: H.125, G.126, D.127 Chain F: R.171 Ligands: IPA.6 Ligand excluded by PLIP SO4.4: 6 residues within 4Å: Chain A: R.8, H.9, K.11, N.46, R.47 Chain B: N.221 Ligand excluded by PLIP SO4.7: 8 residues within 4Å: Chain A: R.47 Chain B: V.24, G.25, R.90, A.91, G.92, S.93 Ligands: MTI.11 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain B: H.125, G.126, D.127 Chain C: R.171 Ligands: IPA.13, IPA.25 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain B: K.103, R.104, D.218 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain B: H.9, K.11, N.46, R.47 Ligand excluded by PLIP SO4.15: 7 residues within 4Å: Chain C: G.25, R.90, A.91, G.92, S.93 Chain D: R.47 Ligands: MTI.18 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain B: R.171 Chain C: H.125, G.126, D.127 Ligands: IPA.14 Ligand excluded by PLIP SO4.17: 6 residues within 4Å: Chain C: R.8, H.9, K.11, N.46, R.47 Chain D: N.221 Ligand excluded by PLIP SO4.19: 7 residues within 4Å: Chain C: R.47 Chain D: G.25, R.90, A.91, G.92, S.93 Ligands: MTI.23 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain D: H.125, G.126, D.127 Chain E: R.171 Ligands: IPA.24 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain D: K.103, R.104, K.213, D.218 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain C: N.221 Chain D: H.9, K.11, N.46, R.47 Ligand excluded by PLIP SO4.26: 7 residues within 4Å: Chain E: G.25, R.90, A.91, G.92, S.93 Chain F: R.47 Ligands: MTI.29 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain D: R.171 Chain E: H.125, G.126, D.127 Ligands: IPA.30 Ligand excluded by PLIP SO4.28: 6 residues within 4Å: Chain E: R.8, H.9, K.11, N.46, R.47 Chain F: N.221 Ligand excluded by PLIP SO4.31: 8 residues within 4Å: Chain E: R.47 Chain F: V.24, G.25, R.90, A.91, G.92, S.93 Ligands: MTI.35 Ligand excluded by PLIP SO4.32: 6 residues within 4Å: Chain A: R.171 Chain F: H.125, G.126, D.127 Ligands: IPA.12, IPA.37 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain F: K.103, R.104, D.218 Ligand excluded by PLIP SO4.34: 4 residues within 4Å: Chain F: H.9, K.11, N.46, R.47 Ligand excluded by PLIP

6 x MTI: 3,4-DIHYDROXY-2-[(METHYLSULFANYL)METHYL]-5-(4-OXO-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)PYRROLIDINIUM(Non-covalent)

MTI.5: 16 residues within 4Å: Chain A: V.68, R.90, S.93, C.94, G.95, Y.162, V.183, E.184, M.185, E.186, D.208, P.211, W.214 Chain B: H.9, V.75 Ligands: SO4.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.185, A:E.186, A:D.208 pi-Stacking: A:Y.162 MTI.11: 17 residues within 4Å: Chain A: H.9, R.47, V.75 Chain B: V.68, R.90, S.93, C.94, G.95, Y.162, V.183, E.184, M.185, E.186, D.208, P.211, W.214 Ligands: SO4.7 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.185, B:E.186, B:D.208, A:R.47 Water bridges: B:S.93, B:S.93 pi-Stacking: B:Y.162 MTI.18: 15 residues within 4Å: Chain C: V.68, R.90, S.93, C.94, G.95, Y.162, V.183, E.184, M.185, E.186, D.208, W.214 Chain D: H.9, V.75 Ligands: SO4.15 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.90, C:M.185, C:E.186, C:D.208 pi-Stacking: C:Y.162 MTI.23: 16 residues within 4Å: Chain C: H.9, V.75 Chain D: V.68, R.90, S.93, C.94, G.95, Y.162, V.183, E.184, M.185, E.186, D.208, P.211, W.214 Ligands: SO4.19 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:M.185, D:E.186, D:D.208 pi-Stacking: D:Y.162 MTI.29: 15 residues within 4Å: Chain E: V.68, R.90, S.93, C.94, G.95, Y.162, V.183, E.184, M.185, E.186, D.208, W.214 Chain F: H.9, V.75 Ligands: SO4.26 6 PLIP interactions: 1 interactions with chain F, 5 interactions with chain E Water bridges: F:R.47, E:S.93 Hydrogen bonds: E:M.185, E:E.186, E:D.208 pi-Stacking: E:Y.162 MTI.35: 16 residues within 4Å: Chain E: H.9, V.75 Chain F: V.68, R.90, S.93, C.94, G.95, Y.162, V.183, E.184, M.185, E.186, D.208, P.211, W.214 Ligands: SO4.31 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:M.185, F:E.186, F:D.208 Water bridges: F:S.93, F:D.208 pi-Stacking: F:Y.162

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

IPA.6: 4 residues within 4Å: Chain A: H.121, H.125 Chain F: R.171 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.125 Water bridges: A:G.126 IPA.12: 5 residues within 4Å: Chain A: R.171 Chain B: R.118, H.121, L.122 Ligands: SO4.32 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.121, B:L.122 Hydrogen bonds: B:R.118 Water bridges: A:R.171 IPA.13: 4 residues within 4Å: Chain B: H.121, H.125 Chain C: R.171 Ligands: SO4.8 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:G.126 Hydrogen bonds: C:R.171 IPA.14: 4 residues within 4Å: Chain B: R.171 Chain C: H.121, H.125 Ligands: SO4.16 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.171 IPA.24: 4 residues within 4Å: Chain D: H.121, H.125 Chain E: R.171 Ligands: SO4.20 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.125 Water bridges: D:G.126 IPA.25: 5 residues within 4Å: Chain C: R.171 Chain D: R.118, H.121, L.122 Ligands: SO4.8 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:H.121, D:L.122 Hydrogen bonds: D:R.118 Water bridges: C:R.171 IPA.30: 4 residues within 4Å: Chain D: R.171 Chain E: H.121, H.125 Ligands: SO4.27 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:H.125 Water bridges: E:G.126 IPA.36: 4 residues within 4Å: Chain E: R.171 Chain F: R.118, H.121, L.122 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain F Water bridges: E:R.171 Hydrophobic interactions: F:H.121, F:L.122 Hydrogen bonds: F:R.118 IPA.37: 4 residues within 4Å: Chain A: R.171 Chain F: H.121, H.125 Ligands: SO4.32 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:H.125 Water bridges: F:G.126

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Uridine phosphorylase putative

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