Research workbench
R. capsulatus cyt BC1 with one fes protein in B position and one in C position (CIII2 B-C)
Analyse R. capsulatus cyt BC1 with one fes protein in B position and one in C position… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XKU
- Type
- protein
- Length
- 1,678 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquinol-cytochrome C reductase iron-sulfur subunit; Cytochrome B; Cytochrome C1
- EC
- 7.1.1.8
- UniProt
- D5ANZ2, D5ANZ3, D5ANZ4
- Ligands
- HEC, FES
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 46% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, R | Ubiquinol-cytochrome C reductase iron-sulfur subunit (EC 7.1.1.8) | protein | 181 | 23% helix, 21% strand | D5ANZ2 |
| C, P | Cytochrome B | protein | 423 | 61% helix, 0% strand | D5ANZ3 |
| D, Q | Cytochrome C1 | protein | 235 | 35% helix, 6% strand | D5ANZ4 |
Ligands and binding sites
- HEC · Heme C · ligand · 6 copies · chains C, D, P, Q
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.83 | 0.87 | 69 | HEC |
| 2 | 669 | 0.83 | 0.87 | 67 | HEC |
| 3 | 480 | 0.80 | 0.87 | 49 | HEC |
| 4 | 508 | 0.79 | 0.86 | 52 | HEC |
| 5 | 746 | 0.76 | 0.81 | 79 | empty |
Interfaces
13 interfaces between chains.
- P–Q · 1612 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1533 Ų buried · 7 hydrogen bonds · protein-protein
- C–P · 1393 Ų buried · 3 hydrogen bonds · protein-protein
- R–P · 1067 Ų buried · 7 hydrogen bonds · protein-protein
- E–Q · 638 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 2 disulfide (heme c attachment, disulfide).
Compared structures
- 6XKU · R. capsulatus cyt bc1 with one FeS protein in b position and one in c position (CIII2 b-c) · the same entry in another collection · chain Q against Q, TM-score 1.00
- D5ANZ3 · AlphaFold monomer V2.0 prediction for cytochrome B (D5ANZ3) · a predicted model of the same protein · chain P against A, TM-score 0.97
- D5ANZ4 · AlphaFold monomer V2.0 prediction for cytochrome C1 (D5ANZ4) · a predicted model of the same protein · chain D against A, TM-score 0.97
- D5ANZ2 · AlphaFold monomer V2.0 prediction for ubiquinol-cytochrome C reductase iron-sulfur… · a predicted model of the same protein · chain E against A, TM-score 0.79
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 D5ANZ2
- Every structure of UniProt D5ANZ3
- Every structure of UniProt D5ANZ4
- Elsewhere: RCSB PDB 6XKU · PDBe 6XKU · UniProt D5ANZ2 · UniProt D5ANZ3 · UniProt D5ANZ4
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