SMTL ID : 2hrm.1

Crystal structure of dUTPase complexed with substrate analogue methylene-dUTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-trimer

Ligands

3 x UC5: 2'-DEOXY-5'-O-[(S)-HYDROXY(PHOSPHONOMETHYL)PHOSPHORYL]URIDINE(Non-covalent)

UC5.1: 13 residues within 4Å: Chain A: M.68, N.84, G.87, L.88, I.89, D.90, Y.93, Q.96, L.97, M.98 Chain C: R.71, S.72, G.73 15 PLIP interactions: 7 interactions with chain C, 8 interactions with chain A Hydrogen bonds: C:R.71, C:S.72, C:G.73, A:N.84, A:L.88, A:D.90, A:M.98, A:M.98 Water bridges: C:D.32, C:R.71, C:R.71, C:L.74, A:D.90 Hydrophobic interactions: A:I.89, A:Y.93 UC5.3: 13 residues within 4Å: Chain A: R.71, S.72, G.73 Chain B: M.68, N.84, G.87, L.88, I.89, D.90, Y.93, Q.96, L.97, M.98 15 PLIP interactions: 7 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:R.71, A:S.72, A:G.73, B:N.84, B:L.88, B:D.90, B:M.98, B:M.98 Water bridges: A:D.32, A:R.71, A:R.71, A:L.74, B:D.90 Hydrophobic interactions: B:I.89, B:Y.93 UC5.5: 13 residues within 4Å: Chain B: R.71, S.72, G.73 Chain C: M.68, N.84, G.87, L.88, I.89, D.90, Y.93, Q.96, L.97, M.98 15 PLIP interactions: 8 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:I.89, C:Y.93 Hydrogen bonds: C:N.84, C:L.88, C:D.90, C:M.98, C:M.98, B:R.71, B:S.72, B:G.73 Water bridges: C:D.90, B:D.32, B:R.71, B:R.71, B:L.74

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: H.76, K.77, H.78, R.104, Q.106, D.107 Chain B: T.48 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.104, A:Q.106, A:D.107, A:D.107, A:D.107, B:T.48 Water bridges: A:R.104 EDO.4: 7 residues within 4Å: Chain B: H.76, K.77, H.78, R.104, Q.106, D.107 Chain C: T.48 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.104, B:Q.106, B:D.107, B:D.107, B:D.107, C:T.48 Water bridges: B:R.104 EDO.6: 7 residues within 4Å: Chain A: T.48 Chain C: H.76, K.77, H.78, R.104, Q.106, D.107 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:T.48, C:R.104, C:Q.106, C:D.107, C:D.107, C:D.107 Water bridges: C:R.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kovari, J. et al., Methylene substitution at the alpha-beta bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site. Proteins (2008)

Release Date

2007-07-31

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Deoxyuridine 5'-triphosphate nucleotidohydrolase

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