SMTL ID : 3phc.1

Crystal Structure of Plasmodium falciparum purine nucleoside phosphorylase in complex with DADMe-ImmG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

3 x K: POTASSIUM ION(Non-covalent)

K.1: 4 residues within 4Å: Chain A: E.47, V.67 Chain B: E.47, V.67 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.47, B:V.67, A:E.47, A:V.67 K.6: 4 residues within 4Å: Chain C: E.47, V.67 Chain D: E.47, V.67 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:E.47, D:V.67, C:E.47, C:V.67, H2O.6 K.11: 4 residues within 4Å: Chain E: E.47, V.67 Chain F: E.47, V.67 5 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: F:E.47, F:V.67, E:E.47, E:V.67, H2O.9

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

PO4.2: 8 residues within 4Å: Chain A: G.24, R.28, R.89, G.91, S.92, E.185 Chain B: R.46 Ligands: IM5.3 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.24, A:S.92, A:S.92, A:S.92 Salt bridges: A:R.28, A:R.89, B:R.46 PO4.4: 8 residues within 4Å: Chain A: R.46 Chain B: G.24, R.28, R.89, G.91, S.92, E.185 Ligands: IM5.5 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.24, B:S.92 Salt bridges: B:R.28, B:R.89, A:R.46 Water bridges: A:R.46 PO4.7: 7 residues within 4Å: Chain C: G.24, R.28, R.89, G.91, S.92 Chain D: R.46 Ligands: IM5.8 8 PLIP interactions: 1 interactions with chain D, 7 interactions with chain C Salt bridges: D:R.46, C:R.28, C:R.89 Hydrogen bonds: C:G.24, C:D.25, C:S.92, C:S.92, C:S.92 PO4.9: 9 residues within 4Å: Chain C: R.46 Chain D: G.24, R.28, R.89, A.90, G.91, S.92, E.185 Ligands: IM5.10 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.24, D:S.92 Salt bridges: D:R.28, D:R.89, C:R.46 PO4.12: 10 residues within 4Å: Chain E: V.23, G.24, D.25, R.28, R.89, G.91, S.92, E.185 Chain F: R.46 Ligands: IM5.13 7 PLIP interactions: 1 interactions with chain F, 6 interactions with chain E Salt bridges: F:R.46, E:R.28, E:R.89 Hydrogen bonds: E:G.24, E:D.25, E:S.92, E:S.92 PO4.14: 7 residues within 4Å: Chain E: R.46 Chain F: G.24, R.28, R.89, G.91, S.92 Ligands: IM5.15 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.24, F:S.92, F:S.92 Salt bridges: F:R.28, F:R.89, E:R.46

6 x IM5: 2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one(Non-covalent)

IM5.3: 15 residues within 4Å: Chain A: V.67, S.92, C.93, G.94, Y.161, V.182, E.183, M.184, E.185, D.207, P.210, W.213 Chain B: H.8, R.46 Ligands: PO4.2 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:M.160, A:E.185, A:D.207, B:H.8, B:R.46 Salt bridges: A:E.185 IM5.5: 15 residues within 4Å: Chain A: H.8, R.46 Chain B: V.67, S.92, C.93, G.94, Y.161, V.182, E.183, M.184, E.185, D.207, P.210, W.213 Ligands: PO4.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.161, B:Y.161, B:E.183, B:E.185, B:D.207 Salt bridges: B:E.185 IM5.8: 14 residues within 4Å: Chain C: V.67, S.92, C.93, G.94, Y.161, V.182, E.183, M.184, E.185, D.207, W.213 Chain D: H.8, R.46 Ligands: PO4.7 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:M.160, C:Y.161, C:Y.161, C:E.185, C:D.207, D:R.46 Water bridges: C:Y.161 Salt bridges: C:E.185 IM5.10: 15 residues within 4Å: Chain C: H.8, R.46 Chain D: V.67, S.92, C.93, G.94, Y.161, V.182, E.183, M.184, E.185, D.207, P.210, W.213 Ligands: PO4.9 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:M.160, D:E.185, D:D.207, C:H.8, C:R.46 Water bridges: D:N.220 Salt bridges: D:E.185 IM5.13: 15 residues within 4Å: Chain E: V.67, S.92, C.93, G.94, Y.161, V.182, E.183, M.184, E.185, D.207, P.210, W.213 Chain F: H.8, R.46 Ligands: PO4.12 6 PLIP interactions: 2 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:H.8, F:R.46, E:M.160, E:E.185, E:D.207 Salt bridges: E:E.185 IM5.15: 16 residues within 4Å: Chain E: H.8, R.46 Chain F: V.67, S.92, C.93, G.94, M.160, Y.161, V.182, E.183, M.184, E.185, D.207, P.210, W.213 Ligands: PO4.14 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:E.183, F:E.185, F:D.207, E:H.8 Water bridges: F:Y.161, F:Y.161 Salt bridges: F:E.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ho, M. et al., Crystal Structure of Plasmodium falciparum purine nucleoside phosphorylase in complex with DADMe-ImmG. To be Published

Release Date

2011-11-09

Peptides

Purine nucleoside phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Purine nucleoside phosphorylase