Research workbench
Cytochrome BC1 complex from chicken with fenamidone bound
Analyse Cytochrome BC1 complex from chicken with fenamidone bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L75
- Type
- protein
- Length
- 4,068 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial ubiquinol-cytochrome-C reductase complex core protein I; Mitochondrial…
- EC
- 1.10.2.2
- UniProt
- D0VX31, D0VX29, P18946, D0VX26, Q5ZLR5, D0VX30, D0VX32, D0VX28, D0VX27
- Ligands
- PEE, HEM, CDL, FNM, UQ, HEC, FES, UNL, AZI
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 17 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitochondrial ubiquinol-cytochrome-C reductase complex core protein I (EC 1.10.2.2) | protein | 443 | 47% helix, 19% strand | D0VX31 |
| B | Mitochondrial ubiquinol-cytochrome-C reductase complex core protein 2 (EC 1.10.2.2) | protein | 421 | 45% helix, 19% strand | D0VX29 |
| C | Cytochrome B (EC 1.10.2.2) | protein | 380 | 71% helix, 2% strand | P18946 |
| D, Q | Mitochondrial cytochrome C1, heme protein (EC 1.10.2.2) | protein | 241 | 39% helix, 8% strand | D0VX26 |
| E, R | Cytochrome B-C1 complex subunit 5, rieske ironsulfur protein, mitochondrial (EC 1.10.2.2) | protein | 196 | 26% helix, 19% strand | Q5ZLR5 |
| F, S | Mitochondrial ubiquinol-cytochrome C reductase 14 kda protein (EC 1.10.2.2) | protein | 101 | 70% helix, 0% strand | D0VX30 |
| G | Mitochondrial ubiquinol-cytochrome C reductase ubiquinone- binding protein qp-C (EC 1.10.2.2) | protein | 81 | 57% helix, 11% strand | D0VX32 |
| H | Mitochondrial ubiquinol-cytochrome C reductase 11 kda protein, complex III subunit VIII (EC 1.10.2.2) | protein | 70 | 71% helix, 0% strand | D0VX28 |
| I | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 46 | 9% helix, 13% strand | Q5ZLR5 |
| J | Mitochondrial ubiquinol-cytochrome C reductase 7.2 kda protein (EC 1.10.2.2) | protein | 61 | 75% helix, 0% strand | D0VX27 |
| N | Mitochondrial ubiquinol-cytochrome-C reductase complex core protein I (EC 1.10.2.2) | protein | 442 | 47% helix, 19% strand | D0VX31 |
| O | Mitochondrial ubiquinol-cytochrome-C reductase complex core protein 2 (EC 1.10.2.2) | protein | 422 | 45% helix, 20% strand | D0VX29 |
| P | Cytochrome B (EC 1.10.2.2) | protein | 379 | 71% helix, 2% strand | P18946 |
| T | Mitochondrial ubiquinol-cytochrome C reductase ubiquinone- binding protein qp-C (EC 1.10.2.2) | protein | 78 | 59% helix, 12% strand | D0VX32 |
| U | Mitochondrial ubiquinol-cytochrome C reductase 11 kda protein, complex III subunit VIII (EC 1.10.2.2) | protein | 67 | 75% helix, 0% strand | D0VX28 |
| V | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 43 | 9% helix, 14% strand | Q5ZLR5 |
| W | Mitochondrial ubiquinol-cytochrome C reductase 7.2 kda protein (EC 1.10.2.2) | protein | 59 | 78% helix, 0% strand | D0VX27 |
Ligands and binding sites
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 6 copies · chains A, C, D, E, J, F, G, N, P, Q, R, W, S, T
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, P
- CDL · Cardiolipin · ligand · 4 copies · chains C, D, F, G, P, Q, S, T
- FNM · (5S)-5-methyl-2-(methylsulfanyl)-5-phenyl-3-(phenylamino)-3,5-dihydro-4H-imidazol-4-one · ligand · 2 copies · chains C, P
- UQ · Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer · ligand · 2 copies · chains C, P
- HEC · Heme C · ligand · 2 copies · chains D, Q
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, R
- UNL · Unknown ligand · ion · 11 copies · chains A, B, C, D, E, P, R, Q
- AZI · Azide ion · ion · 2 copies · chains C, D, P, Q
- BOG · octyl beta-D-glucopyranoside · additive · 6 copies · chains C, G, D, E, J, P, Q, R, W
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 | 543 | 0.87 | 0.93 | 58 | HEM, AZI, UNL |
| 2 | 785 | 0.86 | 0.88 | 74 | HEM, AZI, UNL |
| 3 | 188 | 0.83 | 0.97 | 27 | empty |
| 4 | 176 | 0.83 | 0.98 | 27 | empty |
| 5 | 763 | 0.80 | 0.83 | 75 | BOG, HEM, UQ |
Interfaces
53 interfaces between chains.
- N–O · 2059 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2057 Ų buried · 32 hydrogen bonds · protein-protein
- O–V · 1740 Ų buried · 20 hydrogen bonds · protein-protein
- B–I · 1721 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1606 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 cofactor (disulfide, heme c attachment).
Compared structures
- 3L75 · Cytochrome BC1 complex from chicken with fenamidone bound · the same entry in another collection · chain N against N, 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 D0VX31
- Every structure of UniProt D0VX29
- Every structure of UniProt P18946
- Every structure of UniProt D0VX26
- Every structure of UniProt Q5ZLR5
- Every structure of UniProt D0VX30
- Every structure of UniProt D0VX32
- Every structure of UniProt D0VX28
- Every structure of UniProt D0VX27
- Elsewhere: RCSB PDB 3L75 · PDBe 3L75 · UniProt D0VX31 · UniProt D0VX29 · UniProt P18946 · UniProt D0VX26 · UniProt Q5ZLR5 · UniProt D0VX30 · UniProt D0VX32 · UniProt D0VX28 · UniProt D0VX27
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