SMTL ID : 2hqu.1

Human dUTPase in complex with alpha,beta-iminodUTP and magnesium ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 1 residues within 4Å: Ligands: DUP.3 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain A: D.95 Chain B: D.95 Chain C: D.95 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: R.85 Ligands: DUP.8 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: R.153 Ligands: DUP.5 No protein-ligand interaction detected (PLIP)

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

DUP.3: 15 residues within 4Å: Chain A: P.84, R.85, S.86, G.87, Q.131 Chain B: A.98, G.99, V.100, I.101, D.102, Y.105, N.108, G.110 Chain C: F.158 Ligands: MG.1 19 PLIP interactions: 9 interactions with chain B, 8 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: B:A.98, B:Y.105 Hydrogen bonds: B:G.99, B:V.100, B:V.100, B:D.102, B:G.110, B:G.110, A:R.85, A:R.85, A:S.86, A:S.86, A:S.86, A:G.87, A:Q.131, C:F.158 Water bridges: B:V.112, C:F.158 Salt bridges: A:R.85 DUP.5: 21 residues within 4Å: Chain A: A.98, G.99, V.100, I.101, D.102, Y.105, N.108, V.109, G.110 Chain B: R.153, G.156, G.157, F.158, G.159, S.160, T.161 Chain C: R.85, S.86, G.87, Q.131 Ligands: MG.6 28 PLIP interactions: 8 interactions with chain C, 9 interactions with chain B, 11 interactions with chain A Hydrogen bonds: C:R.85, C:S.86, C:S.86, C:S.86, C:G.87, C:Q.131, B:G.157, B:F.158, B:G.159, B:S.160, B:T.161, B:G.162, A:G.99, A:V.100, A:V.100, A:D.102, A:D.102, A:G.110, A:G.110 Water bridges: C:L.88, B:T.161, B:T.161, A:V.112 Salt bridges: C:R.85, B:R.153 Hydrophobic interactions: A:A.98, A:I.101, A:Y.105 DUP.8: 19 residues within 4Å: Chain A: R.153, G.157, F.158, G.159, S.160, T.161 Chain B: R.85, S.86, G.87, Q.131 Chain C: A.98, G.99, V.100, I.101, D.102, Y.105, N.108, G.110 Ligands: MG.4 28 PLIP interactions: 9 interactions with chain A, 9 interactions with chain B, 10 interactions with chain C Hydrogen bonds: A:F.158, A:G.159, A:S.160, A:T.161, B:R.85, B:R.85, B:S.86, B:S.86, B:S.86, B:G.87, B:Q.131, C:G.99, C:V.100, C:D.102, C:D.102, C:G.110, C:G.110 Water bridges: A:R.153, A:R.153, A:T.161, A:T.161, B:L.88, C:V.112 Salt bridges: A:R.153, B:R.85 Hydrophobic interactions: C:A.98, C:I.101, C:Y.105

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 7 residues within 4Å: Chain C: I.72, A.73, L.74, D.102, E.103, Y.105, R.106 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Varga, B. et al., Active site closure facilitates juxtaposition of reactant atoms for initiation of catalysis by human dUTPase. Febs Lett. (2007)

Release Date

2007-07-24

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Deoxyuridine 5'-triphosphate nucleotidohydrolase

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