SMTL ID : 4k22.1

Structure of the C-terminal truncated form of E.Coli C5-hydroxylase UBII involved in ubiquinone (Q8) biosynthesis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: R.49, V.226, F.269, I.294, Q.300 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.49, A:Q.300 Water bridges: A:Q.300 GOL.2: 7 residues within 4Å: Chain A: Y.329, R.333 Chain D: W.140, A.174, S.281, H.282, L.284 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:Y.329, A:R.333, A:R.333, D:A.174, D:S.281 GOL.5: 6 residues within 4Å: Chain A: M.81, Q.204, H.295, P.296, L.297, A.298 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.204, A:H.295, A:L.297, A:A.298 GOL.7: 6 residues within 4Å: Chain A: F.269, P.270, L.271, T.272, I.294 Ligands: GOL.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.272, A:T.272 Water bridges: A:G.301 GOL.8: 6 residues within 4Å: Chain B: Q.204, H.295, P.296, L.297, A.298, L.356 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.204, B:H.295, B:L.297, B:A.298 GOL.11: 6 residues within 4Å: Chain B: R.49, V.226, F.269, I.294, Q.300 Ligands: GOL.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.49, B:Q.300 Water bridges: B:R.49, B:Q.300 GOL.12: 4 residues within 4Å: Chain B: P.270, L.271, T.272 Ligands: GOL.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.272, B:T.272 Water bridges: B:G.301 GOL.13: 6 residues within 4Å: Chain C: R.49, V.226, F.269, I.294, Q.300 Ligands: GOL.19 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.49, C:Q.300 Water bridges: C:Q.300 GOL.14: 7 residues within 4Å: Chain C: Y.329, R.333 Chain B: W.140, A.174, S.281, H.282, L.284 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Y.329, C:R.333, C:R.333, B:A.174, B:S.281 GOL.17: 6 residues within 4Å: Chain C: M.81, Q.204, H.295, P.296, L.297, A.298 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.204, C:H.295, C:L.297, C:A.298 GOL.19: 6 residues within 4Å: Chain C: F.269, P.270, L.271, T.272, I.294 Ligands: GOL.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.272, C:T.272 Water bridges: C:G.301 GOL.20: 6 residues within 4Å: Chain D: Q.204, H.295, P.296, L.297, A.298, L.356 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.204, D:H.295, D:L.297, D:A.298 GOL.23: 6 residues within 4Å: Chain D: R.49, V.226, F.269, I.294, Q.300 Ligands: GOL.24 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.49, D:Q.300 Water bridges: D:R.49, D:Q.300 GOL.24: 4 residues within 4Å: Chain D: P.270, L.271, T.272 Ligands: GOL.23 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.272, D:T.272 Water bridges: D:G.301

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

CL.3: 4 residues within 4Å: Chain A: G.65, V.66, W.67, Q.68 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: D.175 Chain C: W.181, D.182 Chain D: R.277 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain C: Q.328, Y.329, I.330 Chain B: Y.329, I.330 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: G.65, V.66, W.67, Q.68 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain C: G.65, V.66, W.67, Q.68 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain A: W.181, D.182 Chain C: D.175 Chain B: R.277 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain A: Q.328, Y.329, I.330 Chain D: Y.329, I.330 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain D: G.65, V.66, W.67, Q.68 Ligand excluded by PLIP

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 4 residues within 4Å: Chain A: E.82, W.84, D.254, R.256 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.82 PEG.16: 4 residues within 4Å: Chain C: E.82, W.84, D.254, R.256 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.82

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Chehade, M.H. et al., ubiI, a New Gene in Escherichia coli Coenzyme Q Biosynthesis, Is Involved in Aerobic C5-hydroxylation. J.Biol.Chem. (2013)

Release Date

2013-05-29

Peptides

Protein VisC: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Protein VisC