SMTL ID : 5hhu.1 (2 other biounits)

Plasmodium vivax hypoxanthine-guanine phosphoribosyltransferase in complex with [3R,4R]-4-guanin-9-yl-3-((S)-2-hydroxy-2-phosphonoethyl)oxy-1-N-(phosphonopropionyl)pyrrolidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.149, D.150 Ligands: YPG.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.149, A:E.149, H2O.1, H2O.1, H2O.1 MG.2: 3 residues within 4Å: Chain A: D.209, R.215 Ligands: YPG.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.209, A:D.209, H2O.1 MG.4: 3 residues within 4Å: Chain B: S.84, E.149, D.150 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.149, B:D.150, H2O.1, H2O.1 MG.5: 3 residues within 4Å: Chain B: D.209, R.215 Ligands: YPG.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.209, B:D.209 MG.7: 3 residues within 4Å: Chain C: S.84, E.149, D.150 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.149, C:D.150, H2O.1, H2O.1, H2O.1 MG.8: 3 residues within 4Å: Chain C: D.209, R.215 Ligands: YPG.9 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.209, C:D.209, H2O.1 MG.10: 3 residues within 4Å: Chain D: E.149, D.150 Ligands: YPG.12 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.149, D:E.149, D:D.150, H2O.1 MG.11: 3 residues within 4Å: Chain D: D.209, R.215 Ligands: YPG.12 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.209, D:D.209, H2O.1

4 x YPG: [3-[(3~{R},4~{R})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[(2~{S})-2-oxidanyl-2-phosphono-ethoxy]pyrrolidin-1-yl]-3-oxidanylidene-propyl]phosphonic acid(Non-covalent)

YPG.3: 21 residues within 4Å: Chain A: K.82, G.83, R.117, K.119, E.149, I.151, I.152, D.153, T.154, G.155, K.156, T.157, K.181, A.201, F.202, V.203, L.208, D.209, R.215 Ligands: MG.1, MG.2 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:L.81, A:K.82, A:G.83, A:D.153, A:D.153, A:T.154, A:T.154, A:T.154, A:T.154, A:G.155, A:K.156, A:T.157, A:T.157, A:T.157, A:K.181, A:V.203, A:V.203, A:D.209, A:D.209, A:R.215, A:R.215 Water bridges: A:S.84, A:D.209 YPG.6: 20 residues within 4Å: Chain B: L.81, K.82, G.83, R.117, E.149, I.151, I.152, D.153, T.154, G.155, K.156, T.157, K.181, A.201, F.202, V.203, L.208, D.209, R.215 Ligands: MG.5 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:L.81, B:K.82, B:G.83, B:D.153, B:T.154, B:T.154, B:T.154, B:G.155, B:K.156, B:T.157, B:T.157, B:T.157, B:K.181, B:V.203, B:V.203, B:D.209, B:D.209, B:R.215, B:R.215 YPG.9: 21 residues within 4Å: Chain C: L.81, K.82, G.83, R.117, E.149, I.151, I.152, D.153, T.154, G.155, K.156, T.157, L.158, K.181, A.201, F.202, V.203, L.208, D.209, R.215 Ligands: MG.8 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:L.81, C:K.82, C:G.83, C:R.117, C:D.153, C:T.154, C:T.154, C:T.154, C:G.155, C:T.157, C:L.158, C:K.181, C:V.203, C:V.203, C:D.209, C:R.215, C:R.215 Water bridges: C:D.209 YPG.12: 21 residues within 4Å: Chain D: L.81, K.82, G.83, R.117, E.149, I.151, I.152, D.153, T.154, G.155, K.156, T.157, K.181, A.201, F.202, V.203, L.208, D.209, R.215 Ligands: MG.10, MG.11 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:L.81, D:K.82, D:G.83, D:D.153, D:D.153, D:T.154, D:T.154, D:T.154, D:T.154, D:G.155, D:K.156, D:T.157, D:T.157, D:K.181, D:V.203, D:V.203, D:D.209, D:R.215, D:R.215 Water bridges: D:D.209, D:D.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Keough, D.T. et al., Structure and Inhibition of Plasmodium vivax Hypoxanthine-Guanine Phosphoribosyltransferase: A Novel Approach to the Design of Antimalarial Compounds based on a Central Pyrrolidine Hub. To Be Published

Release Date

2017-01-18

Peptides

Hypoxanthine-guanine-xanthine phosphoribosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Hypoxanthine-guanine-xanthine phosphoribosyltransferase

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