Research workbench
Yeast cytochrome BC1 complex
Analyse Yeast cytochrome BC1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KB9
- Type
- protein
- Length
- 2,180 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquinol-cytochrome C reductase complex core protein I; Ubiquinol-cytochrome C reductase…
- EC
- 1.10.2.2
- UniProt
- P07256, P07257, P00163, P07143, P08067, P00127, P00128, P08525, P22289
- Ligands
- HEM, PEF, PCF, UMQ, SMA, UQ6, PIE, CDL, FES
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 11 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquinol-cytochrome C reductase complex core protein I (EC 1.10.2.2) | protein | 431 | 45% helix, 18% strand | P07256 |
| B | Ubiquinol-cytochrome C reductase complex core protein 2 (EC 1.10.2.2) | protein | 352 | 39% helix, 20% strand | P07257 |
| C | Cytochrome B | protein | 385 | 71% helix, 2% strand | P00163 |
| D | Cytochrome C1, heme protein | protein | 246 | 40% helix, 7% strand | P07143 |
| E | Ubiquinol-cytochrome C reductase iron-sulfur subunit (EC 1.10.2.2) | protein | 185 | 28% helix, 24% strand | P08067 |
| F | Ubiquinol-cytochrome C reductase complex 17 kd protein (EC 1.10.2.2) | protein | 74 | 68% helix, 0% strand | P00127 |
| G | Ubiquinol-cytochrome C reductase complex 14 kd protein (EC 1.10.2.2) | protein | 125 | 70% helix, 0% strand | P00128 |
| H | Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein qp-C (EC 1.10.2.2) | protein | 93 | 38% helix, 11% strand | P08525 |
| I | Ubiquinol-cytochrome C reductase complex 7.3 kd protein (EC 1.10.2.2) | protein | 55 | 65% helix, 0% strand | P22289 |
| J | Heavy chain (vh) of fv-fragment | protein | 127 | 2% helix, 52% strand | — |
| K | Light chain (vl) of fv-fragment | protein | 107 | 0% helix, 43% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains C, D
- PEF · Di-palmitoyl-3-sn-phosphatidylethanolamine · ligand · 2 copies · chains C, G, H
- PCF · 1,2-diacyl-sn-glycero-3-phoshocholine · ligand · chains A, C, D, E
- UMQ · Undecyl-maltoside · ligand · chains A, E, H, I
- SMA · Stigmatellin A · ligand · chains C
- UQ6 · 5-(3,7,11,15,19,23-hexamethyl-tetracosa-2,6,10,14,18, 22-hexaenyl)-2,3-dimethoxy-6-methyl-benzene-1,4-diol · ligand · chains C
- PIE · 1,2-diacyl-sn-glycero-3-phosphoinositol · ligand · chains C, D, E
- CDL · Cardiolipin · ligand · chains C, D, G
- 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 | 732 | 0.84 | 0.87 | 68 | HEM |
| 2 | 167 | 0.82 | 0.97 | 33 | empty |
| 3 | 1035 | 0.79 | 0.80 | 97 | PEF |
| 4 | 508 | 0.79 | 0.86 | 48 | HEM, UQ6 |
| 5 | 975 | 0.77 | 0.79 | 106 | empty |
Interfaces
23 interfaces between chains.
- C–G · 1802 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1722 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1658 Ų buried · 13 hydrogen bonds · protein-protein
- C–H · 1481 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 1218 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 cofactor (disulfide, heme 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 P07256
- Every structure of UniProt P07257
- Every structure of UniProt P00163
- Every structure of UniProt P07143
- Every structure of UniProt P08067
- Every structure of UniProt P00127
- Every structure of UniProt P00128
- Every structure of UniProt P08525
- Every structure of UniProt P22289
- Elsewhere: RCSB PDB 1KB9 · PDBe 1KB9 · UniProt P07256 · UniProt P07257 · UniProt P00163 · UniProt P07143 · UniProt P08067 · UniProt P00127 · UniProt P00128 · UniProt P08525 · UniProt P22289
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