Research workbench
R. capsulatus CIII2CIV tripartite super-complex, conformation B (sc- 1B)
Analyse R. capsulatus CIII2CIV tripartite super-complex, conformation B (sc- 1B) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XKZ
- Type
- protein
- Length
- 2,593 residues
- Chains
- 9
- 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, 1.9.3.1
- UniProt
- D5ANZ2, D5ANZ3, D5ANZ4, D5ARP4, D5ARP5, D5ARP7, Q05389
- Ligands
- HEC, FES, CU
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 6 distinct chains · 55% helix, 4% 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, 22% strand | D5ANZ2 |
| C, P | Cytochrome B | protein | 423 | 61% helix, 0% strand | D5ANZ3 |
| D, Q | Cytochrome C1 | protein | 235 | 35% helix, 6% strand | D5ANZ4 |
| n | Cytochrome C oxidase, CBB3-type, subunit I (EC 1.9.3.1) | protein | 471 | 74% helix, 2% strand | D5ARP4 |
| o | Cytochrome C oxidase, CBB3-type, subunit II (EC 1.9.3.1) | protein | 190 | 53% helix, 1% strand | D5ARP5 |
| p | CBB3-type cytochrome C oxidase subunit CCOP,CYTOCHROME C- type cyt cy | protein | 254 | 56% helix, 2% strand | D5ARP7, Q05389 |
Ligands and binding sites
- HEC · Heme C · ligand · 11 copies · chains C, D, P, Q, n, o, p
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, R
- CU · Copper (II) ion · metal · chains n
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 | 576 | 0.88 | 0.93 | 83 | HEC |
| 2 | 1127 | 0.88 | 0.88 | 125 | HEC |
| 3 | 686 | 0.83 | 0.87 | 67 | HEC |
| 4 | 695 | 0.83 | 0.86 | 69 | HEC |
| 5 | 525 | 0.80 | 0.86 | 51 | HEC |
Interfaces
17 interfaces between chains.
- n–o · 3719 Ų buried · 47 hydrogen bonds · protein-protein
- n–p · 1971 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1647 Ų buried · 7 hydrogen bonds · protein-protein
- P–Q · 1642 Ų buried · 7 hydrogen bonds · protein-protein
- C–P · 1388 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 cofactor, 2 disulfide (heme c attachment, disulfide).
Compared structures
- 6XKZ · R. capsulatus CIII2CIV tripartite super-complex, conformation B (SC-1B) · the same entry in another collection · chain p against p, 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
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
- Every structure of UniProt D5ARP4
- Every structure of UniProt D5ARP5
- Every structure of UniProt D5ARP7
- Every structure of UniProt Q05389
- Elsewhere: RCSB PDB 6XKZ · PDBe 6XKZ · UniProt D5ANZ2 · UniProt D5ANZ3 · UniProt D5ANZ4 · UniProt D5ARP4 · UniProt D5ARP5 · UniProt D5ARP7 · UniProt Q05389
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