Research workbench
Crystal structure analysis of bovine BC1 with methoxy acrylate stilbene (moas)
Analyse Crystal structure analysis of bovine BC1 with methoxy acrylate stilbene (moas) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SQQ
- Type
- protein
- Length
- 2,104 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, P00129, P13271, P00126, P00130, P07552
- Ligands
- HEC, UQ2, OST, FES
- 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 | 73% helix, 2% strand | P00157 |
| D | Cytochrome C1, heme protein, mitochondrial | protein | 241 | 39% helix, 5% 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 | 31% helix, 22% strand | P13272 |
| F | Ubiquinol-cytochrome C reductase complex 14 kda protein (EC 1.10.2.2) | protein | 105 | 69% helix, 1% strand | P00129 |
| G | Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein qp-C (EC 1.10.2.2) | protein | 75 | 53% helix, 12% strand | P13271 |
| H | Ubiquinol-cytochrome C reductase complex 11 kda protein (EC 1.10.2.2) | protein | 70 | 63% 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, 7% strand | P13272 |
| J | Ubiquinol-cytochrome C reductase complex 7.2 kda protein (EC 1.10.2.2) | protein | 59 | 71% helix, 0% strand | P00130 |
| K | Ubiquinol-cytochrome C reductase complex 6.4 kda protein (EC 1.10.2.2) | protein | 54 | 67% helix, 0% strand | P07552 |
Ligands and binding sites
- HEC · Heme C · ligand · 3 copies · chains C, D
- UQ2 · Ubiquinone-2 · ligand · chains C
- OST · Methyl (2Z)-3-methoxy-2-{2-[(E)-2-phenylvinyl]phenyl}acrylate · ligand · chains C
- FES · Fe2/s2 (inorganic) cluster · ligand · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.85 | 0.93 | 47 | HEC |
| 2 | 826 | 0.82 | 0.85 | 96 | empty |
| 3 | 690 | 0.79 | 0.84 | 63 | empty |
| 4 | 515 | 0.79 | 0.85 | 50 | HEC, UQ2 |
| 5 | 722 | 0.79 | 0.82 | 56 | empty |
Interfaces
25 interfaces between chains.
- A–B · 2257 Ų buried · 43 hydrogen bonds · protein-protein
- B–I · 2128 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1733 Ų buried · 18 hydrogen bonds · protein-protein
- A–I · 1446 Ų buried · 18 hydrogen bonds · protein-protein
- C–F · 1250 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1SQQ · Crystal Structure Analysis of Bovine Bc1 with Methoxy Acrylate Stilbene (MOAS) · the same entry in another collection · chain K against K, TM-score 1.00
- P00157 · AlphaFold monomer V2.0 prediction for cytochrome B (P00157) · a predicted model of the same protein · chain C against A, TM-score 1.00
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 P00129
- Every structure of UniProt P13271
- Every structure of UniProt P00126
- Every structure of UniProt P00130
- Every structure of UniProt P07552
- Elsewhere: RCSB PDB 1SQQ · PDBe 1SQQ · UniProt P31800 · UniProt P23004 · UniProt P00157 · UniProt P00125 · UniProt P13272 · UniProt P00129 · UniProt P13271 · UniProt P00126 · UniProt P00130 · UniProt P07552
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