SMTL ID : 3c3i.2 (1 other biounit)

Evolution of chlorella virus dUTPase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-trimer

Ligands

3 x DUD: DEOXYURIDINE-5'-DIPHOSPHATE(Non-covalent)

DUD.1: 15 residues within 4Å: Chain A: A.76, G.77, V.78, I.79, D.80, Y.83, E.86, V.87, K.88, I.90 Chain B: R.131, F.136 Chain C: R.63, S.64, G.65 15 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: A:A.76, A:I.79, A:Y.83 Hydrogen bonds: A:G.77, A:D.80, A:D.80, A:K.88, A:K.88, C:S.64, C:S.64, C:G.65 Water bridges: A:I.90 Salt bridges: B:R.131, C:R.63 pi-Stacking: B:F.136 DUD.2: 13 residues within 4Å: Chain A: R.63, S.64, G.65 Chain B: A.76, G.77, V.78, I.79, D.80, Y.83, E.86, V.87, K.88 Chain C: R.131 12 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A, 7 interactions with chain B Salt bridges: C:R.131 Hydrogen bonds: A:S.64, A:S.64, A:G.65, A:L.66, B:G.77, B:D.80, B:K.88, B:K.88 Hydrophobic interactions: B:A.76, B:I.79, B:Y.83 DUD.3: 15 residues within 4Å: Chain A: R.131, G.135, F.136, G.137 Chain B: R.63, S.64, G.65 Chain C: A.76, G.77, V.78, I.79, D.80, Y.83, E.86, K.88 14 PLIP interactions: 7 interactions with chain C, 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: C:I.79, C:Y.83 Hydrogen bonds: C:G.77, C:D.80, C:D.80, C:K.88, C:K.88, A:R.131, A:G.137, B:S.64, B:G.65 Salt bridges: A:R.131, B:R.63 pi-Stacking: A:F.136

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: D.73 Chain B: D.73 Chain C: D.73 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Homma, K. et al., Crystallization and crystal-packing studies of Chlorella virus deoxyuridine triphosphatase. Acta Crystallogr.,Sect.F (2009)

Release Date

2009-02-10

Peptides

Deoxyuridine triphosphatase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

Deoxyuridine triphosphatase

Related Entries With Identical Sequence