SMTL ID : 3ehw.1 (1 other biounit)

Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain C: R.153 Ligands: DUP.6 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: D.95 Chain B: D.95 Chain C: D.95 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.95, C:D.95, A:D.95, H2O.5, H2O.8 MG.4: 2 residues within 4Å: Chain A: R.153 Ligands: DUP.2 No protein-ligand interaction detected (PLIP) MG.7: 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.2: 23 residues within 4Å: Chain A: R.153, G.156, G.157, F.158, G.159, S.160, T.161 Chain B: P.84, R.85, S.86, G.87, Q.131 Chain C: A.98, G.99, V.100, I.101, D.102, Y.105, N.108, V.109, G.110, V.112 Ligands: MG.4 26 PLIP interactions: 7 interactions with chain A, 9 interactions with chain B, 10 interactions with chain C Hydrogen bonds: A:G.156, 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:V.100, C:D.102, C:Y.105, C:G.110, C:G.110 Water bridges: A:T.161, B:R.128, C:V.112 Salt bridges: A:R.153, B:R.85 Hydrophobic interactions: C:A.98, C:Y.105 DUP.5: 20 residues within 4Å: Chain A: A.98, G.99, V.100, I.101, D.102, Y.105, N.108, 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.7 26 PLIP interactions: 10 interactions with chain A, 10 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: A:A.98, A:I.101, A:Y.105 Hydrogen bonds: A:G.99, A:V.100, A:V.100, A:D.102, A:G.110, A:G.110, C:R.85, C:R.85, C:S.86, C:S.86, C:S.86, C:G.87, C:Q.131, B:F.158, B:G.159, B:S.160, B:T.161, B:G.162 Water bridges: A:V.112, C:R.128, C:R.128 Salt bridges: C:R.85, B:R.153 DUP.6: 21 residues within 4Å: Chain A: R.85, S.86, G.87, Q.131 Chain B: G.97, A.98, G.99, V.100, I.101, D.102, Y.105, N.108, G.110 Chain C: R.153, G.156, G.157, F.158, G.159, S.160, T.161 Ligands: MG.1 28 PLIP interactions: 9 interactions with chain B, 10 interactions with chain A, 9 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: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:G.157, C:F.158, C:G.159, C:S.160, C:T.161, C:G.162 Water bridges: A:R.85, A:R.128, C:R.153, C:R.153 Salt bridges: A:R.85, C:R.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takacs, E. et al., Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the full-length C-termini in all monomers and suggestion for an additional metal ion binding site. To be Published

Release Date

2008-09-30

Peptides

dUTP pyrophosphatase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

dUTP pyrophosphatase

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