Research workbench
Yeast cytochrome BC1 complex with bound substrate cytochrome C
Analyse Yeast cytochrome BC1 complex with bound substrate cytochrome C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KYO
- Type
- protein
- Length
- 4,460 residues
- Chains
- 23
- 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, P00044
- Ligands
- HEC, SMA, FES
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 12 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Ubiquinol-cytochrome C reductase complex core protein I (EC 1.10.2.2) | protein | 430 | 45% helix, 18% strand | P07256 |
| B, M | Ubiquinol-cytochrome C reductase complex core protein 2 (EC 1.10.2.2) | protein | 352 | 35% helix, 18% strand | P07257 |
| C, N | Cytochrome B | protein | 385 | 71% helix, 2% strand | P00163 |
| D, O | Cytochrome C1, heme protein | protein | 245 | 40% helix, 8% strand | P07143 |
| E, P | Ubiquinol-cytochrome C reductase iron-sulfur subunit (EC 1.10.2.2) | protein | 185 | 25% helix, 23% strand | P08067 |
| F, Q | Ubiquinol-cytochrome C reductase complex 17 kd protein (EC 1.10.2.2) | protein | 74 | 70% helix, 0% strand | P00127 |
| G, R | Ubiquinol-cytochrome C reductase complex 14 kd protein (EC 1.10.2.2) | protein | 125 | 71% helix, 1% strand | P00128 |
| H, S | Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein qp-C (EC 1.10.2.2) | protein | 93 | 38% helix, 9% strand | P08525 |
| I, T | Ubiquinol-cytochrome C reductase complex 7.3 kd protein (EC 1.10.2.2) | protein | 53 | 72% helix, 0% strand | P22289 |
| J, U | Heavy chain (vh) of fv-fragment | protein | 127 | 5% helix, 51% strand | — |
| K, V | Light chain (vl) of fv-fragment | protein | 107 | 0% helix, 36% strand | — |
| W | Cytochrome C, iso-1 | protein | 108 | 37% helix, 0% strand | P00044 |
Ligands and binding sites
- HEC · Heme C · ligand · 7 copies · chains C, D, N, O, W
- SMA · Stigmatellin A · ligand · 2 copies · chains C, P, E, N
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, P
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 | 788 | 0.85 | 0.88 | 89 | HEC |
| 2 | 716 | 0.84 | 0.88 | 69 | HEC |
| 3 | 698 | 0.84 | 0.87 | 69 | HEC |
| 4 | 918 | 0.82 | 0.84 | 104 | empty |
| 5 | 173 | 0.82 | 0.97 | 30 | empty |
Interfaces
68 interfaces between chains.
- N–R · 1818 Ų buried · 8 hydrogen bonds · protein-protein
- C–G · 1814 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1708 Ų buried · 14 hydrogen bonds · protein-protein
- N–O · 1698 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1545 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 6 cofactor, 1 modified (disulfide, heme c attachment, methylation).
Compared structures
- 1KYO · Yeast cytochrome BC1 complex with bound substrate cytochrome C · the same entry in another collection · chain J against J, 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 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
- Every structure of UniProt P00044
- Elsewhere: RCSB PDB 1KYO · PDBe 1KYO · UniProt P07256 · UniProt P07257 · UniProt P00163 · UniProt P07143 · UniProt P08067 · UniProt P00127 · UniProt P00128 · UniProt P08525 · UniProt P22289 · UniProt P00044
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