SMTL ID : 4aoz.1

B. subtilis dUTPase YncF in complex with dU, PPi and Mg (P212121)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-trimer

Ligands

3 x DUR: 2'-DEOXYURIDINE(Non-covalent)

DUR.1: 15 residues within 4Å: Chain A: Q.74, N.76, G.79, V.80, I.81, D.82, Y.85, W.92, F.93, P.95 Chain B: S.64 Chain C: R.135, G.137, L.138 Ligands: POP.9 14 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: A:I.81, A:Y.85 Hydrogen bonds: A:Q.74, A:N.76, A:V.80, A:D.82, A:D.82, A:F.93, A:F.93, B:S.64, C:L.138 Water bridges: A:V.80, A:D.82, C:R.135 DUR.2: 10 residues within 4Å: Chain B: N.76, G.79, V.80, I.81, Y.85, W.92, F.93, P.95 Chain C: S.64 Ligands: ACT.5 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:S.64, B:N.76, B:F.93, B:F.93 Hydrophobic interactions: B:Y.85 Water bridges: B:V.80 DUR.8: 15 residues within 4Å: Chain A: S.64 Chain B: R.135, G.137, L.138 Chain C: Q.74, N.76, G.79, V.80, I.81, D.82, Y.85, W.92, F.93, P.95 Ligands: POP.3 14 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 11 interactions with chain C Hydrogen bonds: A:S.64, B:L.138, C:Q.74, C:N.76, C:V.80, C:D.82, C:D.82, C:F.93, C:F.93 Water bridges: B:R.135, C:D.82 Hydrophobic interactions: C:I.81, C:Y.85 pi-Stacking: C:F.93

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.3: 11 residues within 4Å: Chain A: R.63, S.64, S.65 Chain B: R.135, G.137, L.138, G.139, S.140, T.141 Ligands: MG.4, DUR.8 18 PLIP interactions: 10 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:S.64, A:S.64, A:S.65, B:G.139, B:S.140, B:T.141, B:T.141, B:T.141 Water bridges: A:D.27, A:R.63, A:R.109, A:Q.112, A:Q.112, B:R.135, B:T.141 Salt bridges: A:R.63, A:R.63, B:R.135 POP.9: 11 residues within 4Å: Chain B: R.63, S.64, S.65 Chain C: R.135, G.137, L.138, G.139, S.140, T.141 Ligands: DUR.1, MG.10 15 PLIP interactions: 8 interactions with chain C, 7 interactions with chain B Hydrogen bonds: C:G.139, C:S.140, C:T.141, C:T.141, B:S.64, B:S.64, B:S.65 Water bridges: C:R.135, C:R.135, C:T.141, B:R.109, B:Q.112 Salt bridges: C:R.135, B:R.63, B:R.63

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 2 residues within 4Å: Chain B: R.135 Ligands: POP.3 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain C: R.135 Ligands: POP.9 No protein-ligand interaction detected (PLIP)

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 5 residues within 4Å: Chain B: L.43, N.76, F.93 Chain C: S.64 Ligands: DUR.2 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.64, B:N.76 Hydrophobic interactions: B:L.43 ACT.6: 6 residues within 4Å: Chain C: P.45, L.46, G.47, V.48, F.91, W.92 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.91 Hydrogen bonds: C:L.46, C:G.47

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

CL.7: 6 residues within 4Å: Chain B: H.59, M.78 Chain C: W.25, H.59, R.114, M.116 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcia-Nafria, J. et al., Tying Down the Arm in Bacillus Dutpase: Structure and Mechanism. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-05-01

Peptides

PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF

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