MolNFT v1 · #139889 · protein
Cryo-EM structure of human respiratory complex III (cytochrome BC1 complex)
5XTE · Cytochrome B-C1 complex subunit 8: “Cryo-EM structure of human respiratory complex III (cytochrome BC1 complex)”. Electron microscopy, 6 ligands (CDL, PEE, HEM), 20 pockets (best druggability 0.88). MolNFT v1 #139889 on GenesisL1…
- PDB
- 5XTE
- Type
- protein
- Length
- 4,222 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome B-C1 complex subunit 8; Cytochrome B-C1 complex subunit rieske, mitochondrial…
- EC
- 1.10.2.2
- UniProt
- O14949, P47985, Q9UDW1, P07919, P14927, O14957, P08574, P00156, P22695, P31930
- Ligands
- CDL, PEE, HEM, PLX, FES, HEC
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 11 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, N | Cytochrome B-C1 complex subunit 8 | protein | 81 | 65% helix, 4% strand | O14949 |
| B, O | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 57 | 5% helix, 5% strand | P47985 |
| C, P | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 196 | 30% helix, 20% strand | P47985 |
| D, Q | Cytochrome B-C1 complex subunit 9 | protein | 62 | 69% helix, 0% strand | Q9UDW1 |
| E, R | Cytochrome B-C1 complex subunit 6, mitochondrial | protein | 74 | 70% helix, 0% strand | P07919 |
| F, S | Cytochrome B-C1 complex subunit 7 | protein | 106 | 68% helix, 0% strand | P14927 |
| G, T | Cytochrome B-C1 complex subunit 10 | protein | 51 | 69% helix, 0% strand | O14957 |
| H, U | Cytochrome C1, heme protein, mitochondrial | protein | 241 | 41% helix, 3% strand | P08574 |
| J, V | Cytochrome B | protein | 378 | 72% helix, 2% strand | P00156 |
| K, W | Cytochrome B-C1 complex subunit 2, mitochondrial | protein | 419 | 45% helix, 17% strand | P22695 |
| L, Y | Cytochrome B-C1 complex subunit 1, mitochondrial | protein | 446 | 44% helix, 13% strand | P31930 |
Ligands and binding sites
- CDL · Cardiolipin · ligand · 9 copies · chains A, F, J, C, G, V, H, P, T, L, N, S, U, Y
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 6 copies · chains C, D, H, J, A, L, P, Q, U, V, N, T, Y
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains J, V
- PLX · (9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2lambda~5~-aza-6lambda~5~-phosphaoctacosane-6,6,11-triol · ligand · 3 copies · chains C, D, H, J, L, P, Q, U, V, Y, T
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains C, P
- HEC · Heme C · ligand · 2 copies · chains H, P, C, U
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 | 627 | 0.88 | 0.93 | 70 | empty |
| 2 | 1111 | 0.87 | 0.89 | 155 | empty |
| 3 | 750 | 0.84 | 0.87 | 77 | HEM |
| 4 | 828 | 0.84 | 0.86 | 82 | HEM |
| 5 | 1150 | 0.83 | 0.84 | 106 | empty |
Interfaces
65 interfaces between chains.
- K–L · 2226 Ų buried · 28 hydrogen bonds · protein-protein
- W–Y · 2162 Ų buried · 27 hydrogen bonds · protein-protein
- O–W · 2147 Ų buried · 12 hydrogen bonds · protein-protein
- B–K · 2140 Ų buried · 14 hydrogen bonds · protein-protein
- U–V · 1667 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 5XTE · Cryo-EM structure of human respiratory complex III (cytochrome bc1 complex) · the same entry in another collection · chain L against L, TM-score 1.00
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 O14949
- Every structure of UniProt P47985
- Every structure of UniProt Q9UDW1
- Every structure of UniProt P07919
- Every structure of UniProt P14927
- Every structure of UniProt O14957
- Every structure of UniProt P08574
- Every structure of UniProt P00156
- Every structure of UniProt P22695
- Every structure of UniProt P31930
- Elsewhere: RCSB PDB 5XTE · PDBe 5XTE · UniProt O14949 · UniProt P47985 · UniProt Q9UDW1 · UniProt P07919 · UniProt P14927 · UniProt O14957 · UniProt P08574 · UniProt P00156 · UniProt P22695 · UniProt P31930
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