MolNFT v1 · #55386 · protein
X-ray structure of the dimeric cytochrome BC1 complex from the soil bacterium paracoccus denitrificans at 2.7 ångström resolution
2YIU: “X-ray structure of the dimeric cytochrome BC1 complex from the soil bacterium paracoccus denitrificans at 2.7…”. X-ray diffraction, 4 ligands (HEM, SMA, HEC), 20 pockets (best druggability 0.86). MolNFT v1 #55386 on GenesisL1: 3D…
- PDB
- 2YIU
- Type
- protein
- Length
- 1,616 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome B; Cytochrome C1, heme protein; Ubiquinol-cytochrome C reductase iron-sulfur…
- EC
- 1.10.2.2
- UniProt
- P05418, P13627, P05417
- Ligands
- HEM, SMA, HEC, FES
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Cytochrome B (EC 1.10.2.2) | protein | 428 | 68% helix, 2% strand | P05418 |
| B, E | Cytochrome C1, heme protein (EC 1.10.2.2) | protein | 206 | 43% helix, 7% strand | P13627 |
| C, F | Ubiquinol-cytochrome C reductase iron-sulfur subunit (EC 1.10.2.2) | protein | 174 | 21% helix, 25% strand | P05417 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, D
- SMA · Stigmatellin A · ligand · 2 copies · chains A, F, C, D
- HEC · Heme C · ligand · 2 copies · chains B, E
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 645 | 0.86 | 0.90 | 68 | HEM |
| 2 | 627 | 0.86 | 0.90 | 62 | HEM |
| 3 | 430 | 0.80 | 0.87 | 46 | HEM |
| 4 | 439 | 0.79 | 0.87 | 47 | HEM |
| 5 | 453 | 0.77 | 0.84 | 48 | SMA |
Interfaces
9 interfaces between chains.
- A–B · 1654 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1635 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1581 Ų buried · 25 hydrogen bonds · protein-protein
- A–F · 1318 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1300 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 2 disulfide (heme c attachment, disulfide).
Compared structures
- 2YIU · X-ray structure of the dimeric cytochrome BC1 complex from the soil bacterium paracoccus… · the same entry in another collection · chain F against F, TM-score 1.00
- P05418 · AlphaFold monomer V2.0 prediction for cytochrome B (P05418) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P13627 · AlphaFold monomer V2.0 prediction for cytochrome C1 (P13627) · a predicted model of the same protein · chain E against A, TM-score 0.99
- P05417 · AlphaFold monomer V2.0 prediction for ubiquinol-cytochrome C reductase iron-sulfur… · a predicted model of the same protein · chain C 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 P05418
- Every structure of UniProt P13627
- Every structure of UniProt P05417
- Elsewhere: RCSB PDB 2YIU · PDBe 2YIU · UniProt P05418 · UniProt P13627 · UniProt P05417
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