MolNFT v1 · #37359 · protein
Crystal structure of bovine heart mitochondrial BC1 with JG144 inhibitor
2FYU · Ubiquinol-cytochrome-C reductase complex core protein I…: “Crystal structure of bovine heart mitochondrial BC1 with JG144 inhibitor”. X-ray diffraction, 3 ligands (HEM, FDN, FES), 20 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 2FYU
- Type
- protein
- Length
- 2,099 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquinol-cytochrome-C reductase complex core protein I, mitochondrial…
- EC
- 1.10.2.2
- UniProt
- P31800, P23004, P00157, P00125, P13272, P00129, P13271, P00126, P00130, P07552
- Ligands
- HEM, FDN, FES
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 11 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquinol-cytochrome-C reductase complex core protein I, mitochondrial (EC 1.10.2.2) | protein | 446 | 46% helix, 19% strand | P31800 |
| B | Ubiquinol-cytochrome-C reductase complex core protein 2, mitochondrial (EC 1.10.2.2) | protein | 423 | 45% helix, 20% strand | P23004 |
| C | Cytochrome B | protein | 378 | 72% helix, 2% strand | P00157 |
| D | Cytochrome C1, heme protein, mitochondrial | protein | 241 | 40% helix, 5% strand | P00125 |
| E | Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial (EC 1.10.2.2) | protein | 196 | 30% helix, 19% strand | P13272 |
| F | Hypothetical protein LOC616871 | protein | 106 | 75% helix, 0% strand | P00129 |
| G | Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein qp-C (EC 1.10.2.2) | protein | 75 | 53% helix, 11% strand | P13271 |
| H | Ubiquinol-cytochrome C reductase complex 11 kda protein (EC 1.10.2.2) | protein | 64 | 77% helix, 0% strand | P00126 |
| I | Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial | protein | 57 | 12% helix, 14% strand | P13272 |
| J | Ubiquinol-cytochrome C reductase complex 7.2 kda protein (EC 1.10.2.2) | protein | 60 | 68% helix, 0% strand | P00130 |
| K | Ubiquinol-cytochrome C reductase complex 6.4 kda protein (EC 1.10.2.2) | protein | 53 | 70% helix, 0% strand | P07552 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains C, D
- FDN · (5S)-3-anilino-5-(2,4-difluorophenyl)-5-methyl-1,3-oxazolidine-2,4-dione · ligand · chains C
- FES · Fe2/s2 (inorganic) cluster · ligand · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 647 | 0.83 | 0.87 | 67 | HEM |
| 2 | 1134 | 0.80 | 0.81 | 92 | empty |
| 3 | 640 | 0.80 | 0.85 | 64 | empty |
| 4 | 500 | 0.80 | 0.86 | 53 | HEM |
| 5 | 897 | 0.79 | 0.81 | 91 | empty |
Interfaces
19 interfaces between chains.
- A–B · 2370 Ų buried · 34 hydrogen bonds · protein-protein
- B–I · 2202 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1730 Ų buried · 18 hydrogen bonds · protein-protein
- A–I · 1460 Ų buried · 20 hydrogen bonds · protein-protein
- C–F · 1285 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
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 P31800
- Every structure of UniProt P23004
- Every structure of UniProt P00157
- Every structure of UniProt P00125
- Every structure of UniProt P13272
- Every structure of UniProt P00129
- Every structure of UniProt P13271
- Every structure of UniProt P00126
- Every structure of UniProt P00130
- Every structure of UniProt P07552
- Elsewhere: RCSB PDB 2FYU · PDBe 2FYU · UniProt P31800 · UniProt P23004 · UniProt P00157 · UniProt P00125 · UniProt P13272 · UniProt P00129 · UniProt P13271 · UniProt P00126 · UniProt P00130 · UniProt P07552
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