SMTL ID : 5knp.2 (2 other biounits)

Crystal structure of Mycobacterium tuberculosis hypoxanthine guanine phosphoribosyltransferase in complex with [3S,4R]-(4-(Hypoxanthin-9-yl)pyrrolidin-3-yl)-oxymethanephosphonic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 x 6W7: [(3~{S},4~{R})-4-(6-oxidanylidene-1~{H}-purin-9-yl)pyrrolidin-3-yl]oxymethylphosphonic acid(Non-covalent)

6W7.1: 12 residues within 4Å: Chain A: V.129, V.130, D.131, S.132, G.133, K.159, D.179, F.180, V.181, L.186, D.187 Ligands: POP.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:D.131, A:S.132, A:S.132, A:S.132, A:G.133, A:K.159, A:V.181, A:V.181 Water bridges: A:L.134, A:L.134, A:T.135, A:D.187 pi-Stacking: A:F.180 6W7.5: 12 residues within 4Å: Chain B: V.129, V.130, D.131, S.132, G.133, K.159, D.179, F.180, V.181, L.186, D.187 Ligands: POP.8 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.131, B:S.132, B:S.132, B:S.132, B:G.133, B:K.159, B:V.181, B:V.181 Water bridges: B:L.134, B:T.135, B:D.187 pi-Stacking: B:F.180

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.187, R.193 Ligands: POP.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.187, H2O.1, H2O.1, H2O.1 MG.3: 2 residues within 4Å: Chain A: E.127, D.128 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.128, H2O.1, H2O.1, H2O.2, H2O.2 MG.6: 3 residues within 4Å: Chain B: D.187, R.193 Ligands: POP.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.187, H2O.3, H2O.3, H2O.3 MG.7: 3 residues within 4Å: Chain B: A.73, E.127, D.128 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.127, B:D.128, B:D.128, H2O.3, H2O.3

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.4: 7 residues within 4Å: Chain A: L.70, K.71, G.72, D.187, R.193 Ligands: 6W7.1, MG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.71, A:G.72 Water bridges: A:A.73, A:D.187, A:D.187, A:R.193, A:R.193, A:R.193 Salt bridges: A:R.193 POP.8: 7 residues within 4Å: Chain B: L.70, K.71, G.72, D.187, R.193 Ligands: 6W7.5, MG.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.71, B:G.72 Water bridges: B:A.73, B:D.187, B:R.193, B:R.193, B:R.193, B:R.193 Salt bridges: B:R.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eng, W.S. et al., Crystal structure of Mycobacterium tuberculosis hypoxanthine guanine phosphoribosyltransferase in complex with pyrrolidine nucleoside phosphonate. To Be Published

Release Date

2017-09-20

Peptides

Hypoxanthine-guanine phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hypoxanthine-guanine phosphoribosyltransferase

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