SMTL ID : 2cje.1

THE CRYSTAL STRUCTURE OF A COMPLEX OF Leishmania major DUTPASE WITH SUBSTRATE ANALOGUE DUPNHP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-dimer

Ligands

2 x DUN: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-DIPHOSPHATE(Non-covalent)

DUN.1: 22 residues within 4Å: Chain A: Q.21, L.24, N.25, I.28, W.41, E.48, E.51, D.79, H.82, F.83, K.179, N.183, R.186, Y.191, K.198, N.206 Chain B: K.59, W.60, W.61 Ligands: MG.2, MG.3, MG.4 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.28, A:H.82, A:F.83, A:F.83, B:W.61 Hydrogen bonds: A:N.25, A:E.51, A:D.79, A:K.179, A:N.183, A:R.186, A:R.186, A:Y.191, A:K.198, A:N.206, B:K.59 Water bridges: A:Y.191, A:Y.191 pi-Stacking: B:W.61, B:W.61 DUN.5: 22 residues within 4Å: Chain A: K.59, W.60, W.61 Chain B: Q.21, L.24, N.25, I.28, W.41, E.48, E.51, D.79, H.82, F.83, K.179, N.183, R.186, Y.191, K.198, N.206 Ligands: MG.6, MG.7, MG.8 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.28, B:H.82, B:F.83, B:F.83, A:W.61 Hydrogen bonds: B:N.25, B:E.51, B:D.79, B:H.82, B:K.179, B:N.183, B:R.186, B:R.186, B:Y.191, B:Y.191, B:K.198, B:N.206, A:K.59 Water bridges: B:E.48 pi-Stacking: A:W.61, A:W.61

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.48, E.51 Ligands: DUN.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.48, A:E.51, H2O.1, H2O.1 MG.3: 7 residues within 4Å: Chain A: E.48, E.51, E.76, D.79 Ligands: DUN.1, MG.2, MG.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.48, A:E.51, A:E.76, A:D.79, H2O.4 MG.4: 4 residues within 4Å: Chain A: E.51, E.76 Ligands: DUN.1, MG.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.76, H2O.2, H2O.2, H2O.4, H2O.4 MG.6: 4 residues within 4Å: Chain B: E.48, E.51 Ligands: DUN.5, MG.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.48, B:E.51, H2O.4, H2O.4 MG.7: 7 residues within 4Å: Chain B: E.48, E.51, E.76, D.79 Ligands: DUN.5, MG.6, MG.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.48, B:E.51, B:E.76, B:D.79, H2O.7 MG.8: 4 residues within 4Å: Chain B: E.51, E.76 Ligands: DUN.5, MG.7 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.76, H2O.5, H2O.5, H2O.7, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hemsworth, G.R. et al., The Crystal Structure of the Leishmania Major Deoxyuridine Triphosphate Nucleotidohydrolase in Complex with Nucleotide Analogues, Dump, and Deoxyuridine. J.Biol.Chem. (2011)

Release Date

2007-04-17

Peptides

DUTPASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DUTPASE