SMTL ID : 4rhy.1 (2 other biounits)

Crystal structures of Mycobacterium tuberculosis 6-oxopurine phosphoribosyltransferase which is a potential target for drug development against this disease

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: E.121, D.122 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.121, A:D.122, H2O.1, H2O.2, H2O.3 MG.2: 2 residues within 4Å: Chain A: D.181 Ligands: 3QG.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.181, H2O.1, H2O.1, H2O.1, H2O.2 MG.4: 2 residues within 4Å: Chain B: E.121, D.122 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.122, H2O.3, H2O.3, H2O.5, H2O.5 MG.5: 2 residues within 4Å: Chain B: D.181 Ligands: 3QG.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.181, H2O.3, H2O.3, H2O.3 MG.7: 2 residues within 4Å: Chain C: E.121, D.122 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.121, C:D.122, H2O.5, H2O.5, H2O.7 MG.8: 2 residues within 4Å: Chain C: D.181 Ligands: 3QG.9 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.181, H2O.5, H2O.5, H2O.5, H2O.7 MG.10: 2 residues within 4Å: Chain D: E.121, D.122 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.121, D:D.122, H2O.7, H2O.7, H2O.7 MG.11: 2 residues within 4Å: Chain D: D.181 Ligands: 3QG.12 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.181, H2O.7, H2O.8, H2O.9, H2O.10

4 x 3QG: [2-({2-[bis(2-phosphonoethyl)amino]ethyl}[2-(6-oxo-3,6-dihydro-9H-purin-9-yl)ethyl]amino)ethyl]phosphonic acid(Non-covalent)

3QG.3: 19 residues within 4Å: Chain A: L.64, K.65, G.66, S.91, V.123, V.124, D.125, S.126, G.127, L.128, T.129, K.153, D.173, F.174, V.175, L.180, D.181, R.187 Ligands: MG.2 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:K.65, A:G.66, A:S.91, A:S.91, A:S.91, A:D.125, A:D.125, A:S.126, A:G.127, A:L.128, A:T.129, A:T.129, A:K.153, A:V.175, A:R.187, A:R.187 Water bridges: A:K.65, A:K.65, A:A.67, A:L.130, A:D.181, A:D.181, A:D.181, A:D.181, A:D.181 pi-Stacking: A:F.174 3QG.6: 17 residues within 4Å: Chain B: L.64, K.65, G.66, V.123, V.124, D.125, S.126, G.127, L.128, T.129, K.153, D.173, F.174, V.175, D.181, R.187 Ligands: MG.5 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:K.65, B:G.66, B:S.91, B:S.91, B:D.125, B:D.125, B:D.125, B:S.126, B:G.127, B:L.128, B:T.129, B:T.129, B:K.153, B:V.175, B:R.187, B:R.187 Water bridges: B:A.67, B:D.181, B:D.181, B:D.181 pi-Stacking: B:F.174 3QG.9: 19 residues within 4Å: Chain C: L.64, K.65, G.66, S.91, V.123, V.124, D.125, S.126, G.127, L.128, T.129, K.153, D.173, F.174, V.175, L.180, D.181, R.187 Ligands: MG.8 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:L.64, C:L.64, C:K.65, C:G.66, C:S.91, C:S.91, C:D.125, C:D.125, C:S.126, C:G.127, C:L.128, C:T.129, C:T.129, C:T.129, C:K.153, C:V.175, C:R.187, C:R.187 Water bridges: C:S.126, C:S.126, C:L.130, C:D.181 3QG.12: 19 residues within 4Å: Chain D: L.64, K.65, G.66, S.91, V.123, V.124, D.125, S.126, G.127, L.128, T.129, K.153, D.173, F.174, V.175, L.180, D.181, R.187 Ligands: MG.11 23 PLIP interactions: 23 interactions with chain D Hydrogen bonds: D:K.65, D:G.66, D:S.91, D:S.91, D:D.125, D:D.125, D:S.126, D:G.127, D:L.128, D:T.129, D:T.129, D:T.129, D:K.153, D:V.175, D:D.181, D:R.187, D:R.187 Water bridges: D:S.126, D:S.126, D:L.130, D:D.181, D:D.181, D:D.181

Links

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Citation

Eng, W.S. et al., First Crystal Structures of Mycobacterium tuberculosis 6-Oxopurine Phosphoribosyltransferase: Complexes with GMP and Pyrophosphate and with Acyclic Nucleoside Phosphonates Whose Prodrugs Have Antituberculosis Activity. J.Med.Chem. (2015)

Release Date

2015-05-20

Peptides

Hypoxanthine-guanine phosphoribosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Hypoxanthine-guanine phosphoribosyltransferase

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