Research workbench
Rhodobacter capsulatus cytochrome BC1 complex with stigmatellin bound
Analyse Rhodobacter capsulatus cytochrome BC1 complex with stigmatellin bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZRT
- Type
- protein
- Length
- 1,724 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome B; Cytochrome C1; Ubiquinol-cytochrome C reductase iron-sulfur subunit
- EC
- 7.1.1.8
- UniProt
- D5ANZ3, D5ANZ4, D5ANZ2
- Ligands
- HEM, UNL, SMA, HEC, FES
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, P | Cytochrome B | protein | 431 | 62% helix, 1% strand | D5ANZ3 |
| D, Q | Cytochrome C1 | protein | 248 | 35% helix, 3% strand | D5ANZ4 |
| E, R | Ubiquinol-cytochrome C reductase iron-sulfur subunit (EC 7.1.1.8) | protein | 183 | 16% helix, 26% strand | D5ANZ2 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, P
- UNL · Unknown ligand · ligand · 4 copies · chains C, D, E, P, Q, R
- SMA · Stigmatellin A · ligand · 2 copies · chains C, R, E, P
- HEC · Heme C · ligand · 2 copies · chains D, Q
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, R
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · chains P, Q, 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 | 396 | 0.86 | 0.95 | 46 | HEM |
| 2 | 381 | 0.85 | 0.93 | 46 | HEM |
| 3 | 931 | 0.82 | 0.83 | 98 | HEM, UNL, PG6 |
| 4 | 924 | 0.81 | 0.83 | 92 | HEM, UNL |
| 5 | 1023 | 0.78 | 0.80 | 110 | HEC |
Interfaces
11 interfaces between chains.
- C–D · 2035 Ų buried · 18 hydrogen bonds · protein-protein
- P–Q · 1985 Ų buried · 15 hydrogen bonds · protein-protein
- C–P · 1613 Ų buried · 25 hydrogen bonds · protein-protein
- E–P · 1257 Ų buried · 7 hydrogen bonds · protein-protein
- C–R · 1245 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 4 disulfide, 1 covalent (heme c attachment, disulfide, covalent ligand).
Compared structures
- 1ZRT · Rhodobacter capsulatus cytochrome bc1 complex with stigmatellin bound · the same entry in another collection · chain R against R, TM-score 1.00
- D5ANZ3 · AlphaFold monomer V2.0 prediction for cytochrome B (D5ANZ3) · a predicted model of the same protein · chain C against A, TM-score 0.99
- D5ANZ4 · AlphaFold monomer V2.0 prediction for cytochrome C1 (D5ANZ4) · a predicted model of the same protein · chain Q against A, TM-score 0.95
- 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 0.92
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 D5ANZ3
- Every structure of UniProt D5ANZ4
- Every structure of UniProt D5ANZ2
- Elsewhere: RCSB PDB 1ZRT · PDBe 1ZRT · UniProt D5ANZ3 · UniProt D5ANZ4 · UniProt D5ANZ2
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