Research workbench
Crystal structure analysis of bovine BC1 with myxothiazol
Analyse Crystal structure analysis of bovine BC1 with myxothiazol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SQP
- Type
- protein
- Length
- 2,102 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquinol-cytochrome-C reductase complex core protein I, mitochondrial precursor…
- EC
- 1.10.2.2
- UniProt
- P31800, P23004, P00157, P00125, P13272, P13271, P00126, P00130, P07552
- Ligands
- CDL, PEE, HEC, MYX, FES, PLX
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 11 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquinol-cytochrome-C reductase complex core protein I, mitochondrial precursor (EC 1.10.2.2) | protein | 446 | 46% helix, 19% strand | P31800 |
| B | Ubiquinol-cytochrome-C reductase complex core protein 2, mitochondrial precursor (EC 1.10.2.2) | protein | 423 | 45% helix, 20% strand | P23004 |
| C | Cytochrome B | protein | 378 | 72% helix, 2% strand | P00157 |
| D | Cytochrome C1, heme protein, mitochondrial | protein | 241 | 36% helix, 7% strand | P00125 |
| E | Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp) [contains: ubiquinol-cytochrome C reductase 8 kda protein (complex III subunit IX)] | protein | 196 | 29% helix, 16% strand | P13272 |
| F | SUB6 | protein | 105 | 64% helix, 1% strand | — |
| G | Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein qp-C (EC 1.10.2.2) | protein | 75 | 51% helix, 12% strand | P13271 |
| H | Ubiquinol-cytochrome C reductase complex 11 kda protein (EC 1.10.2.2) | protein | 67 | 67% helix, 0% strand | P00126 |
| I | Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp) [contains: ubiquinol-cytochrome C reductase 8 kda protein (complex III subunit IX)] | protein | 57 | 0% helix, 11% strand | P13272 |
| J | Ubiquinol-cytochrome C reductase complex 7.2 kda protein (EC 1.10.2.2) | protein | 61 | 75% helix, 0% strand | P00130 |
| K | Ubiquinol-cytochrome C reductase complex 6.4 kda protein (EC 1.10.2.2) | protein | 53 | 68% helix, 0% strand | P07552 |
Ligands and binding sites
- CDL · Cardiolipin · ligand · 3 copies · chains A, C, K, D, F, G
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 3 copies · chains A, C, E, F, G, D, J
- HEC · Heme C · ligand · 3 copies · chains C, D
- MYX · (2Z,6E)-7-{2'-[(2E,4E)-1,6-dimethylhepta-2,4-dienyl]-2, 4'-bi-1,3-thiazol-4-yl}-3,5-dimethoxy-4-methylhepta-2, 6-dienamide · ligand · chains C
- FES · Fe2/s2 (inorganic) cluster · ligand · chains E
- PLX · (9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2lambda~5~-aza-6lambda~5~-phosphaoctacosane-6,6,11-triol · ligand · chains A, C, D, E, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.85 | 0.93 | 44 | HEC |
| 2 | 1044 | 0.81 | 0.82 | 102 | PLX |
| 3 | 492 | 0.80 | 0.87 | 52 | HEC |
| 4 | 601 | 0.79 | 0.84 | 53 | empty |
| 5 | 713 | 0.78 | 0.82 | 55 | PEE |
Interfaces
25 interfaces between chains.
- A–B · 2309 Ų buried · 41 hydrogen bonds · protein-protein
- B–I · 2154 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1758 Ų buried · 14 hydrogen bonds · protein-protein
- A–I · 1469 Ų buried · 17 hydrogen bonds · protein-protein
- C–F · 1270 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 cofactor (disulfide, heme c attachment).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P31800
- Every structure of UniProt P23004
- Every structure of UniProt P00157
- Every structure of UniProt P00125
- Every structure of UniProt P13272
- Every structure of UniProt P13271
- Every structure of UniProt P00126
- Every structure of UniProt P00130
- Every structure of UniProt P07552
- Elsewhere: RCSB PDB 1SQP · PDBe 1SQP · UniProt P31800 · UniProt P23004 · UniProt P00157 · UniProt P00125 · UniProt P13272 · UniProt P13271 · UniProt P00126 · UniProt P00130 · UniProt P07552
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