Research workbench
Crystal structure analysis of bovine BC1 with uhdbt
Analyse Crystal structure analysis of bovine BC1 with uhdbt in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SQV
- Type
- protein
- Length
- 2,100 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…
- EC
- 1.10.2.2
- UniProt
- P31800, P23004, P00157, P00125, P13272, P00129, P13271, P00126, P00130, P07552
- Ligands
- HEC, UHD, UQ2, FES
- Pockets
- 20 · best druggability 0.86
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 (EC 1.10.2.2) | protein | 446 | 45% helix, 19% strand | P31800 |
| B | Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial (EC 1.10.2.2) | protein | 423 | 45% helix, 20% strand | P23004 |
| C | Cytochrome B (EC 1.10.2.2) | protein | 378 | 74% helix, 2% strand | P00157 |
| D | Cytochrome C1, heme protein, mitochondrial (EC 1.10.2.2) | protein | 241 | 38% helix, 5% strand | P00125 |
| E | Ubiquinol-cytochrome C reductase iron-sulfur subunit (EC 1.10.2.2) | protein | 196 | 27% helix, 19% strand | P13272 |
| F | Ubiquinol-cytochrome C reductase complex 14 kda protein (EC 1.10.2.2) | protein | 105 | 64% helix, 1% strand | P00129 |
| G | Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein qp-C (EC 1.10.2.2) | protein | 75 | 48% helix, 12% strand | P13271 |
| H | Ubiquinol-cytochrome C reductase complex 11 kda protein (EC 1.10.2.2) | protein | 67 | 72% helix, 0% strand | P00126 |
| I | Ubiquinol-cytochrome C reductase complex 8 kda protein (EC 1.10.2.2) | protein | 57 | 7% helix, 11% strand | P13272 |
| J | Ubiquinol-cytochrome C reductase complex 7.2 kda protein (EC 1.10.2.2) | protein | 61 | 70% helix, 0% strand | P00130 |
| K | Ubiquinol-cytochrome C reductase complex 6.4 kda protein (EC 1.10.2.2) | protein | 51 | 63% helix, 0% strand | P07552 |
Ligands and binding sites
- HEC · Heme C · ligand · 3 copies · chains C, D
- UHD · 6-hydroxy-5-undecyl-1,3-benzothiazole-4,7-dione · ligand · chains C
- UQ2 · Ubiquinone-2 · 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.86 | 0.93 | 57 | HEC |
| 2 | 834 | 0.82 | 0.84 | 100 | empty |
| 3 | 511 | 0.80 | 0.86 | 50 | HEC, UQ2 |
| 4 | 649 | 0.79 | 0.84 | 54 | empty |
| 5 | 666 | 0.79 | 0.84 | 59 | empty |
Interfaces
24 interfaces between chains.
- A–B · 2315 Ų buried · 38 hydrogen bonds · protein-protein
- B–I · 2058 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1734 Ų buried · 14 hydrogen bonds · protein-protein
- A–I · 1484 Ų buried · 19 hydrogen bonds · protein-protein
- C–F · 1248 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
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 P00129
- Every structure of UniProt P13271
- Every structure of UniProt P00126
- Every structure of UniProt P00130
- Every structure of UniProt P07552
- Elsewhere: RCSB PDB 1SQV · PDBe 1SQV · UniProt P31800 · UniProt P23004 · UniProt P00157 · UniProt P00125 · UniProt P13272 · UniProt P00129 · UniProt P13271 · UniProt P00126 · UniProt P00130 · UniProt P07552
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