SMTL ID : 2yay.1

The Crystal Structure of Leishmania major dUTPase in complex with substrate analogue dUpNpp

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

2 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)

DUP.1: 22 residues within 4Å: Chain A: Q.24, L.27, N.28, I.31, W.44, E.51, E.54, D.82, H.85, F.86, K.182, N.186, R.189, Y.194, K.201, N.209 Chain B: K.62, W.63, W.64, K.65 Ligands: CA.2, CA.3 26 PLIP interactions: 19 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:I.31, A:H.85, A:F.86, A:F.86, B:W.64 Hydrogen bonds: A:Q.24, A:N.28, A:D.82, A:K.182, A:N.186, A:R.189, A:R.189, A:Y.194, A:Y.194, A:N.209, B:K.62 Water bridges: A:E.54, A:E.54, A:E.54, A:E.54, B:K.62 Salt bridges: A:K.201, B:K.62, B:K.65 pi-Stacking: B:W.64, B:W.64 DUP.4: 22 residues within 4Å: Chain A: K.62, W.63, W.64, K.65 Chain B: Q.24, L.27, N.28, I.31, W.44, E.51, E.54, D.82, H.85, F.86, K.182, N.186, R.189, Y.194, K.201, N.209 Ligands: CA.5, CA.6 23 PLIP interactions: 16 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:I.31, B:H.85, B:F.86, B:F.86, A:W.64 Hydrogen bonds: B:Q.24, B:N.28, B:H.85, B:K.182, B:N.186, B:R.189, B:R.189, B:Y.194, B:Y.194, B:N.209, A:K.62 Water bridges: B:E.51, A:K.62 Salt bridges: B:K.201, A:K.62, A:K.65 pi-Stacking: A:W.64, A:W.64

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: E.51, E.54 Ligands: DUP.1, CA.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.51, A:E.54, A:E.54, H2O.1 CA.3: 6 residues within 4Å: Chain A: E.51, E.54, E.79, D.82 Ligands: DUP.1, CA.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.51, A:E.54, A:E.79, A:D.82, H2O.1 CA.5: 4 residues within 4Å: Chain B: E.51, E.54 Ligands: DUP.4, CA.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.51, B:E.54, B:E.54, H2O.3 CA.6: 6 residues within 4Å: Chain B: E.51, E.54, E.79, D.82 Ligands: DUP.4, CA.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.51, B:E.54, B:E.79, B:D.82, H2O.4

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

2011-03-16

Peptides

DUTPASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DUTPASE

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