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

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 2.03 Å

Oligo State

homo-tetramer

Ligands

4 x 3QF: [2-([2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl]{2-[(2-oxoethyl)(2-phosphonoethyl)amino]ethyl}amino)ethyl]phosphonic acid(Non-covalent)

3QF.1: 21 residues within 4Å: Chain A: V.63, L.64, K.65, G.66, V.89, 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, MG.3 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:K.65, A:G.66, 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:V.175, A:V.175, A:D.181, A:R.187, A:R.187 Water bridges: A:A.67, A:V.89, A:D.122, A:D.122, A:V.123, A:S.126, A:S.126, A:G.127, A:L.130 3QF.4: 23 residues within 4Å: Chain B: V.63, L.64, K.65, G.66, V.89, S.90, D.122, 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.5, MG.6 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:K.65, B:G.66, 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:V.175, B:V.175, B:D.181, B:R.187, B:R.187 Water bridges: B:K.65, B:A.67, B:V.89, B:D.122, B:S.126, B:S.126, B:S.126, B:L.130, B:G.179 pi-Stacking: B:F.174 3QF.7: 21 residues within 4Å: Chain C: V.63, L.64, K.65, G.66, V.89, S.90, 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.9 24 PLIP interactions: 24 interactions with chain C Hydrogen bonds: C:K.65, C:G.66, C:D.125, C:D.125, C:S.126, C:G.127, C:L.128, C:T.129, C:T.129, C:K.153, C:V.175, C:V.175, C:V.175, C:D.181, C:R.187, C:R.187 Water bridges: C:A.67, C:S.91, C:D.122, C:S.126, C:G.127, C:T.129, C:L.130, C:G.179 3QF.10: 21 residues within 4Å: Chain D: V.63, L.64, K.65, G.66, V.89, 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, MG.12 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:K.65, D:G.66, D:D.125, D:S.126, D:G.127, D:L.128, D:T.129, D:K.153, D:V.175, D:V.175, D:D.181, D:D.181, D:D.181, D:R.187, D:R.187 Water bridges: D:K.65, D:K.65, D:A.67, D:V.89, D:V.123, D:S.126, D:S.126, D:L.130, D:G.179, D:D.181

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.181 Ligands: 3QF.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.181, H2O.1, H2O.1, H2O.1, H2O.8 MG.3: 3 residues within 4Å: Chain A: E.121, D.122 Ligands: 3QF.1 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.121, A:D.122, H2O.1, H2O.1, H2O.1, H2O.8 MG.5: 2 residues within 4Å: Chain B: D.181 Ligands: 3QF.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.181, H2O.8, H2O.8, H2O.8, H2O.8 MG.6: 3 residues within 4Å: Chain B: E.121, D.122 Ligands: 3QF.4 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.121, B:D.122, H2O.8, H2O.8, H2O.8, H2O.8 MG.8: 2 residues within 4Å: Chain C: E.121, D.122 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.121, C:D.122, H2O.12, H2O.12, H2O.12, H2O.13 MG.9: 2 residues within 4Å: Chain C: D.181 Ligands: 3QF.7 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.181, H2O.12, H2O.13, H2O.13, H2O.16 MG.11: 3 residues within 4Å: Chain D: E.121, D.122 Ligands: 3QF.10 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.121, D:D.122, H2O.16, H2O.16, H2O.17, H2O.17 MG.12: 3 residues within 4Å: Chain D: D.181, R.187 Ligands: 3QF.10 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.181, H2O.17, H2O.17, H2O.17, H2O.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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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