Research workbench
Complex III2 from candida albicans, inhibitor free, rieske head domain in intermediate position
Analyse Complex III2 from candida albicans, inhibitor free, rieske head domain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RJC
- Type
- protein
- Length
- 1,907 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquinol--cytochrome-C reductase subunit; Cytochrome B; Ubiquinol--cytochrome-C…
- EC
- 7.1.1.8
- UniProt
- A0A1D8PP59, P0C8L0, A0A1D8PHA3, Q5ABS1, A0A1D8PHA2, A0A1D8PJT8, A0A1D8PLP3, P83782, A0A1D8PJX3
- Ligands
- HEM, U10, HEC, FES
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 10 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquinol--cytochrome-C reductase subunit | protein | 416 | 47% helix, 16% strand | A0A1D8PP59 |
| K | Cytochrome B | protein | 383 | 72% helix, 2% strand | P0C8L0 |
| D | Ubiquinol--cytochrome-C reductase catalytic subunit | protein | 244 | 41% helix, 8% strand | A0A1D8PHA3 |
| G | Cytochrome B-C1 complex subunit 7 | protein | 122 | 68% helix, 1% strand | Q5ABS1 |
| F | Ubiquinol--cytochrome-C reductase subunit 8 | protein | 85 | 55% helix, 7% strand | A0A1D8PHA2 |
| H | Ubiquinol--cytochrome-C reductase subunit 6 | protein | 72 | 75% helix, 0% strand | A0A1D8PJT8 |
| I | Ubiquinol--cytochrome-C reductase subunit 9 | protein | 39 | 82% helix, 0% strand | A0A1D8PLP3 |
| B | Cytochrome B-C1 complex subunit 2, mitochondrial | protein | 364 | 41% helix, 19% strand | P83782 |
| M | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 7.1.1.8) | protein | 50 | 68% helix, 0% strand | A0A1D8PJX3 |
| E | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 7.1.1.8) | protein | 132 | 15% helix, 21% strand | A0A1D8PJX3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains K
- U10 · Ubiquinone-10 · ligand · 2 copies · chains K
- HEC · Heme C · ligand · chains D
- 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 | 564 | 0.82 | 0.87 | 65 | HEM |
| 2 | 459 | 0.77 | 0.85 | 50 | HEM, U10 |
| 3 | 890 | 0.77 | 0.80 | 86 | HEC |
| 4 | 751 | 0.75 | 0.79 | 74 | empty |
| 5 | 1072 | 0.73 | 0.76 | 113 | empty |
Interfaces
19 interfaces between chains.
- K–G · 1837 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1796 Ų buried · 13 hydrogen bonds · protein-protein
- K–D · 1748 Ų buried · 16 hydrogen bonds · protein-protein
- K–F · 1376 Ų buried · 5 hydrogen bonds · protein-protein
- D–H · 1137 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor, 1 covalent, 1 disulfide (heme c attachment, heme attachment, covalent ligand, disulfide).
Compared structures
- 7RJC · Complex III2 from Candida albicans, inhibitor free, Rieske head domain in intermediate… · the same entry in another collection · chain E against E, TM-score 1.00
- P0C8L0 · AlphaFold monomer V2.0 prediction for cytochrome B (P0C8L0) · a predicted model of the same protein · chain K against A, TM-score 0.99
- P83782 · AlphaFold monomer V2.0 prediction for cytochrome B-C1 complex subunit 2, mitochondrial… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 A0A1D8PP59
- Every structure of UniProt P0C8L0
- Every structure of UniProt A0A1D8PHA3
- Every structure of UniProt Q5ABS1
- Every structure of UniProt A0A1D8PHA2
- Every structure of UniProt A0A1D8PJT8
- Every structure of UniProt A0A1D8PLP3
- Every structure of UniProt P83782
- Every structure of UniProt A0A1D8PJX3
- Elsewhere: RCSB PDB 7RJC · PDBe 7RJC · UniProt A0A1D8PP59 · UniProt P0C8L0 · UniProt A0A1D8PHA3 · UniProt Q5ABS1 · UniProt A0A1D8PHA2 · UniProt A0A1D8PJT8 · UniProt A0A1D8PLP3 · UniProt P83782 · UniProt A0A1D8PJX3
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