SMTL ID : 3epw.1

Crystal structure of Trypanosoma vivax nucleoside hydrolase in complex with the inhibitor (2R,3R,4S)-1-[(4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-2-(hydroxymethyl)pyrrolidin-3,4-diol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.21, D.26, T.148, D.272 Ligands: JMQ.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.21, A:D.26, A:D.26, A:T.148, A:D.272 CA.4: 5 residues within 4Å: Chain B: D.21, D.26, T.148, D.272 Ligands: JMQ.5 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.21, B:D.26, B:D.26, B:T.148, B:D.272

2 x JMQ: 7-(((2R,3R,4S)-3,4-dihydroxy-2-(hydroxymethyl)pyrrolidin-1-yl)methyl)-3H-pyrrolo[3,2-d]pyrimidin-4(5H)-one(Non-covalent)

JMQ.2: 17 residues within 4Å: Chain A: N.23, D.25, D.26, D.51, F.90, W.94, T.148, M.175, N.184, E.195, W.196, N.197, R.263, Y.268, W.271, D.272 Ligands: CA.1 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.184, A:N.184, A:E.195, A:W.196, A:N.197, A:R.263, A:R.263, A:D.272 Salt bridges: A:D.21, A:D.25, A:D.51, A:D.272 pi-Stacking: A:W.94, A:W.94, A:W.94, A:Y.268 JMQ.5: 17 residues within 4Å: Chain B: N.23, D.25, D.26, D.51, F.90, W.94, T.148, M.175, N.184, E.195, W.196, N.197, R.263, Y.268, W.271, D.272 Ligands: CA.4 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:D.51, B:N.184, B:N.184, B:W.196, B:N.197, B:R.263, B:R.263, B:D.272 Salt bridges: B:D.21, B:D.25, B:D.51, B:D.272 pi-Stacking: B:W.94, B:W.94, B:W.94, B:Y.268

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: D.191 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.191, H2O.1, H2O.1, H2O.1 MG.6: 1 residues within 4Å: Chain B: N.70 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:N.70, H2O.21, H2O.22, H2O.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Versees, W. et al., Crystal structures of T. vivax nucleoside hydrolase in complex with new potent and specific inhibitors. Biochim.Biophys.Acta (2009)

Release Date

2009-03-24

Peptides

IAG-nucleoside hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

IAG-nucleoside hydrolase

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