Research workbench
Yeast cytochrome BC1 complex with stigmatellin
Analyse Yeast cytochrome BC1 complex with stigmatellin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IBZ
- Type
- protein
- Length
- 2,179 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquinol-cytochrome-C reductase complex core protein 1; Ubiquinol-cytochrome-C reductase…
- EC
- 1.10.2.2
- UniProt
- P07256, P07257, P00163, P07143, P08067, P00127, P00128, P08525, P22289
- Ligands
- HEC, UQ6, SMA, FES
- Pockets
- 20 · best druggability 0.85
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 1 (EC 1.10.2.2) | protein | 431 | 44% helix, 18% strand | P07256 |
| B | Ubiquinol-cytochrome-C reductase complex core protein 2 (EC 1.10.2.2) | protein | 352 | 38% helix, 20% strand | P07257 |
| C | Cytochrome B (EC 1.10.2.2) | protein | 385 | 71% helix, 2% strand | P00163 |
| D | Cytochrome C1, heme protein, mitochondrial precursor (EC 1.10.2.2) | protein | 245 | 40% helix, 7% strand | P07143 |
| E | Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) | protein | 185 | 28% helix, 24% strand | P08067 |
| H | Ubiquinol-cytochrome C reductase complex 17 kda protein (EC 1.10.2.2) | protein | 74 | 68% helix, 0% strand | P00127 |
| F | Ubiquinol-cytochrome C reductase complex 14 kda protein (EC 1.10.2.2) | protein | 125 | 70% helix, 0% strand | P00128 |
| G | Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein qp-C (EC 1.10.2.2) | protein | 93 | 41% helix, 11% strand | P08525 |
| I | Ubiquinol-cytochrome C reductase complex 7.3 kda protein (EC 1.10.2.2) | protein | 55 | 69% helix, 0% strand | P22289 |
| X | Variable heavy chain of antibody fragment | protein | 127 | 2% helix, 52% strand | — |
| Y | Variable light chain of antibody fragment | protein | 107 | 0% helix, 42% strand | — |
Ligands and binding sites
- HEC · Heme C · ligand · 3 copies · chains C, D
- 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, E
- SMA · Stigmatellin A · 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 | 643 | 0.85 | 0.89 | 65 | HEC |
| 2 | 172 | 0.82 | 0.97 | 34 | empty |
| 3 | 1021 | 0.80 | 0.81 | 99 | empty |
| 4 | 502 | 0.79 | 0.86 | 47 | HEC, UQ6 |
| 5 | 346 | 0.77 | 0.88 | 34 | empty |
Interfaces
24 interfaces between chains.
- C–F · 1809 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1723 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1651 Ų buried · 14 hydrogen bonds · protein-protein
- C–G · 1477 Ų buried · 9 hydrogen bonds · protein-protein
- D–H · 1227 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 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 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 2IBZ · PDBe 2IBZ · UniProt P07256 · UniProt P07257 · UniProt P00163 · UniProt P07143 · UniProt P08067 · UniProt P00127 · UniProt P00128 · UniProt P08525 · UniProt P22289
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