SMTL ID : 6aps.1

Trypanosoma brucei hypoxanthine guanine phosphoribosyltransferase in complex with [(2-((Guanine-9H-yl)methyl)propane-1,3 diyl)bis(oxy)]bis(methylene))diphosphonic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

2 x SV2: [{2-[(guanine-9-yl)methyl]propane-1,3-diyl}bis(oxymethylene)]bis(phosphonic acid)(Non-covalent)

SV2.1: 20 residues within 4Å: Chain A: L.59, K.60, G.61, E.119, D.120, I.121, L.122, D.123, T.124, A.125, L.126, T.127, K.151, V.171, F.172, V.173, L.178, D.179, R.185 Ligands: MG.2 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:K.60, A:G.61, A:D.120, A:D.123, A:T.124, A:T.124, A:T.124, A:A.125, A:L.126, A:T.127, A:T.127, A:K.151, A:V.173, A:V.173, A:D.179, A:R.185, A:R.185 Water bridges: A:T.124, A:T.124, A:L.128, A:D.179, A:D.179, A:D.179 SV2.6: 20 residues within 4Å: Chain B: L.59, K.60, G.61, E.119, D.120, I.121, L.122, D.123, T.124, A.125, L.126, T.127, K.151, V.171, F.172, V.173, L.178, D.179, R.185 Ligands: MG.7 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:K.60, B:G.61, B:D.120, B:D.123, B:T.124, B:T.124, B:T.124, B:A.125, B:L.126, B:T.127, B:T.127, B:V.173, B:D.179, B:D.179, B:D.179, B:D.179, B:R.185, B:R.185 Water bridges: B:T.124, B:T.124, B:L.128, B:K.151, B:D.179, B:D.179, B:Q.182

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.179 Ligands: SV2.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.179, H2O.1, H2O.1, H2O.5, H2O.5 MG.7: 3 residues within 4Å: Chain B: D.179, R.185 Ligands: SV2.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.179, H2O.8, H2O.8, H2O.12

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 9 residues within 4Å: Chain A: E.23, H.27, D.68, R.188 Chain B: H.27, D.68, R.71, I.72 Ligands: PEG.8 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.31, A:R.188, A:R.188 PEG.8: 8 residues within 4Å: Chain A: H.27, D.68, R.71, I.72 Chain B: E.23, H.27, R.188 Ligands: PEG.3 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.27, B:R.188, B:R.188

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 4 residues within 4Å: Chain A: R.129, P.158, F.159, T.160 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.129, A:R.129, A:P.158, A:T.160, A:T.160 TRS.9: 8 residues within 4Å: Chain A: P.48, G.74, P.79 Chain B: Y.13, F.15, Y.184, E.186, V.187 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:T.80, A:T.80, B:R.188 Hydrogen bonds: B:E.186, B:E.186

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 6 residues within 4Å: Chain A: D.40, Y.41, C.44, H.114, S.142, K.144 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.142 Salt bridges: A:H.114, A:K.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dolezelova, E. et al., Evaluation of the Trypanosoma brucei 6-oxopurine salvage pathway as a potential target for drug discovery. PLoS Negl Trop Dis (2018)

Release Date

2018-03-14

Peptides

Hypoxanthine-guanine phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hypoxanthine-guanine phosphoribosyltransferase

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