SMTL ID : 3enz.1

Arsenolytic structure of Plasmodium falciparum purine nucleoside phosphorylase with hypoxanthine, ribose and arsenate ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-hexamer

Ligands

6 x HPA: HYPOXANTHINE(Non-covalent)

HPA.1: 10 residues within 4Å: Chain A: S.91, C.92, G.93, Y.160, V.181, E.182, M.183, D.206, W.212 Ligands: R1X.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.206 pi-Stacking: A:Y.160 HPA.12: 11 residues within 4Å: Chain B: S.91, C.92, G.93, Y.160, V.181, E.182, M.183, D.206, P.209, W.212 Ligands: R1X.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.206 Water bridges: B:Y.160 HPA.18: 11 residues within 4Å: Chain C: S.91, C.92, G.93, Y.160, V.181, E.182, M.183, D.206, P.209, W.212 Ligands: R1X.19 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.206 Water bridges: C:Y.160 HPA.28: 11 residues within 4Å: Chain D: S.91, C.92, G.93, Y.160, V.181, E.182, M.183, D.206, P.209, W.212 Ligands: R1X.29 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.206 Water bridges: D:Y.160 HPA.38: 10 residues within 4Å: Chain E: S.91, C.92, G.93, Y.160, V.181, E.182, M.183, D.206, W.212 Ligands: R1X.39 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.206 Water bridges: E:Y.160 HPA.42: 10 residues within 4Å: Chain F: S.91, C.92, G.93, Y.160, V.181, E.182, M.183, D.206, W.212 Ligands: R1X.43 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.206

6 x R1X: 1,4-anhydro-D-ribitol(Non-covalent)

R1X.2: 11 residues within 4Å: Chain A: V.66, R.88, S.91, Y.160, E.182, M.183, E.184 Chain B: H.7, R.45 Ligands: HPA.1, ART.3 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:H.7, B:R.45, A:M.183, A:E.184, A:E.184 R1X.13: 11 residues within 4Å: Chain A: H.7, R.45 Chain B: V.66, R.88, S.91, Y.160, E.182, M.183, E.184 Ligands: HPA.12, ART.14 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:M.183, B:E.184, B:E.184, A:H.7, A:R.45 Water bridges: B:S.91, B:Y.160 R1X.19: 11 residues within 4Å: Chain C: V.66, R.88, S.91, Y.160, E.182, M.183, E.184 Chain E: H.7, R.45 Ligands: HPA.18, ART.20 9 PLIP interactions: 3 interactions with chain E, 6 interactions with chain C Hydrogen bonds: E:H.7, E:R.45, E:R.45, C:R.88, C:E.182, C:M.183, C:E.184, C:E.184 Water bridges: C:Y.160 R1X.29: 11 residues within 4Å: Chain D: V.66, R.88, S.91, Y.160, E.182, M.183, E.184 Chain F: H.7, R.45 Ligands: HPA.28, ART.30 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:H.7, F:R.45, F:R.45, D:M.183, D:E.184, D:E.184 R1X.39: 11 residues within 4Å: Chain C: H.7, R.45 Chain E: V.66, R.88, S.91, Y.160, E.182, M.183, E.184 Ligands: HPA.38, ART.40 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain C Hydrogen bonds: E:E.182, E:M.183, E:E.184, E:E.184, C:H.7, C:R.45, C:R.45 R1X.43: 11 residues within 4Å: Chain D: H.7, R.45 Chain F: V.66, R.88, S.91, Y.160, E.182, M.183, E.184 Ligands: HPA.42, ART.44 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain F Hydrogen bonds: D:H.7, D:R.45, D:R.45, F:M.183, F:E.184, F:E.184

6 x ART: ARSENATE(Non-covalent)

ART.3: 10 residues within 4Å: Chain A: V.22, G.23, R.27, R.88, A.89, G.90, S.91, E.184 Chain B: R.45 Ligands: R1X.2 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.23, A:D.24, A:R.27, A:R.27, A:R.88, A:R.88, A:S.91, A:S.91, A:S.91, B:R.45, B:R.45 ART.14: 10 residues within 4Å: Chain A: R.45 Chain B: V.22, G.23, R.27, R.88, A.89, G.90, S.91, E.184 Ligands: R1X.13 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.23, B:D.24, B:R.27, B:R.27, B:R.88, B:R.88, B:S.91, B:S.91, B:S.91, A:R.45, A:R.45 ART.20: 10 residues within 4Å: Chain C: V.22, G.23, R.27, R.88, A.89, G.90, S.91, E.184 Chain E: R.45 Ligands: R1X.19 10 PLIP interactions: 2 interactions with chain E, 8 interactions with chain C Hydrogen bonds: E:R.45, E:R.45, C:G.23, C:R.27, C:R.27, C:R.88, C:R.88, C:S.91, C:S.91, C:S.91 ART.30: 10 residues within 4Å: Chain D: V.22, G.23, R.27, R.88, A.89, G.90, S.91, E.184 Chain F: R.45 Ligands: R1X.29 10 PLIP interactions: 2 interactions with chain F, 8 interactions with chain D Hydrogen bonds: F:R.45, F:R.45, D:G.23, D:R.27, D:R.27, D:R.88, D:R.88, D:S.91, D:S.91, D:S.91 ART.40: 10 residues within 4Å: Chain C: R.45 Chain E: V.22, G.23, R.27, R.88, A.89, G.90, S.91, E.184 Ligands: R1X.39 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:G.23, E:D.24, E:R.27, E:R.27, E:R.88, E:R.88, E:S.91, E:S.91, E:S.91, C:R.45, C:R.45 ART.44: 8 residues within 4Å: Chain D: R.45 Chain F: V.22, G.23, R.88, A.89, G.90, S.91 Ligands: R1X.43 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain F Hydrogen bonds: D:R.45, D:R.45, F:G.23, F:R.88, F:R.88, F:S.91, F:S.91, F:S.91

24 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 5 residues within 4Å: Chain A: E.76, L.121, L.194, R.195 Chain B: N.163 Ligand excluded by PLIP FMT.5: 1 residues within 4Å: Chain A: Y.244 Ligand excluded by PLIP FMT.6: 4 residues within 4Å: Chain A: R.116 Chain B: D.115, R.116, H.119 Ligand excluded by PLIP FMT.7: 3 residues within 4Å: Chain A: S.168, P.209, F.210 Ligand excluded by PLIP FMT.8: 3 residues within 4Å: Chain A: V.129, G.130, T.193 Ligand excluded by PLIP FMT.9: 3 residues within 4Å: Chain A: E.77, Q.80, N.81 Ligand excluded by PLIP FMT.10: 4 residues within 4Å: Chain A: Q.96, S.174, K.175, N.177 Ligand excluded by PLIP FMT.15: 5 residues within 4Å: Chain A: N.163 Chain B: E.76, L.121, L.194, R.195 Ligand excluded by PLIP FMT.16: 2 residues within 4Å: Chain B: Q.80, N.81 Ligand excluded by PLIP FMT.21: 5 residues within 4Å: Chain C: E.76, L.121, L.194, R.195 Chain E: N.163 Ligand excluded by PLIP FMT.22: 5 residues within 4Å: Chain C: P.25, G.26, D.29, Y.43, K.48 Ligand excluded by PLIP FMT.23: 3 residues within 4Å: Chain C: S.168, P.209, F.210 Ligand excluded by PLIP FMT.24: 3 residues within 4Å: Chain C: E.77, Q.80, N.81 Ligand excluded by PLIP FMT.25: 4 residues within 4Å: Chain A: N.109 Chain C: V.129, G.130, T.193 Ligand excluded by PLIP FMT.26: 3 residues within 4Å: Chain C: R.116, H.119 Chain E: R.116 Ligand excluded by PLIP FMT.31: 4 residues within 4Å: Chain B: I.153 Chain D: G.130, T.193 Ligands: NA.17 Ligand excluded by PLIP FMT.32: 3 residues within 4Å: Chain D: Y.43 Chain F: G.26 Ligands: NA.37 Ligand excluded by PLIP FMT.33: 5 residues within 4Å: Chain D: E.76, L.121, L.194, R.195 Chain F: N.163 Ligand excluded by PLIP FMT.34: 3 residues within 4Å: Chain D: H.119, G.124 Ligands: FMT.35 Ligand excluded by PLIP FMT.35: 4 residues within 4Å: Chain D: R.116, H.119 Chain F: R.116 Ligands: FMT.34 Ligand excluded by PLIP FMT.41: 6 residues within 4Å: Chain C: N.163 Chain E: E.76, L.121, I.191, L.194, R.195 Ligand excluded by PLIP FMT.45: 2 residues within 4Å: Chain F: H.119, G.124 Ligand excluded by PLIP FMT.46: 5 residues within 4Å: Chain D: N.163 Chain F: E.76, L.121, L.194, R.195 Ligand excluded by PLIP FMT.47: 2 residues within 4Å: Chain F: E.77, N.81 Ligand excluded by PLIP

5 x NA: SODIUM ION(Non-functional Binders)

NA.11: 4 residues within 4Å: Chain A: E.46, V.66 Chain B: E.46, V.66 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.46, A:V.66, A:V.66, B:E.46, B:V.66 Water bridges: A:G.70 NA.17: 4 residues within 4Å: Chain B: N.109 Chain D: G.130, D.131 Ligands: FMT.31 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:F.132, B:N.109, B:N.109 NA.27: 4 residues within 4Å: Chain C: E.46, V.66 Chain E: E.46, V.66 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:V.66, E:E.46 Water bridges: C:G.70 NA.36: 4 residues within 4Å: Chain D: E.46, V.66 Chain F: E.46, V.66 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:E.46, F:V.66, D:E.46, D:E.46 Water bridges: D:G.70 NA.37: 5 residues within 4Å: Chain D: Y.43, R.45 Chain F: P.25, Y.43 Ligands: FMT.32 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:R.45 Water bridges: F:G.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaikuad, A. et al., Conservation of structure and activity in Plasmodium purine nucleoside phosphorylases. Bmc Struct.Biol. (2009)

Release Date

2009-08-04

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

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