SMTL ID : 4rhu.1 (1 other biounit)

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 2.57 Å

Oligo State

homo-tetramer

Ligands

2 x 3QE: {[(2R)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)propane-1,2-diyl]bis(oxyethane-2,1-diyl)}bis(phosphonic acid)(Non-covalent)

3QE.1: 17 residues within 4Å: Chain A: L.64, K.65, G.66, D.122, V.123, D.125, S.126, G.127, L.128, T.129, K.153, D.173, F.174, V.175, L.180, D.181, R.187 14 PLIP interactions: 14 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 3QE.3: 17 residues within 4Å: Chain B: L.64, K.65, G.66, V.123, V.124, D.125, S.126, G.127, T.129, K.153, D.173, F.174, V.175, L.180, D.181, R.187 Ligands: MG.5 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:K.65, B:G.66, B:V.123, 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:L.130

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: V.63, E.121, D.122 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.121, A:E.121, A:D.122, H2O.1 MG.4: 2 residues within 4Å: Chain B: E.121, D.122 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.121, B:D.122, H2O.1, H2O.2, H2O.2 MG.5: 3 residues within 4Å: Chain B: D.181, R.187 Ligands: 3QE.3 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.181, H2O.2 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.2, H2O.2, H2O.2 MG.9: 3 residues within 4Å: Chain D: E.121, D.122 Ligands: 45T.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.122

2 x 45T: {[(2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)propane-1,2-diyl]bis(oxyethane-2,1-diyl)}bis(phosphonic acid)(Non-covalent)

45T.6: 15 residues within 4Å: Chain C: 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 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:D.125, C:D.125, C:S.126, C:G.127, C:L.128, C:T.129, C:K.153, C:V.175, C:V.175, C:V.175, C:D.181, C:R.187 Water bridges: C:T.129, C:L.130, C:L.130 45T.8: 16 residues within 4Å: Chain D: K.65, 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 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:K.65, 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:R.187, D:R.187

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 Hpt: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Hypoxanthine-guanine phosphoribosyltransferase Hpt

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