Research workbench
Cytochrome BC1 complex from chicken with designed inhibitor bound
Analyse Cytochrome BC1 complex from chicken with designed inhibitor bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U3F
- Type
- protein
- Length
- 4,063 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, Y52, U10, HEC, FES
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 16 distinct chains · 50% 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 | 44% helix, 19% strand | D0VX31 |
| B | Mitochondrial ubiquinol-cytochrome-C reductase complex core protein 2 (EC 1.10.2.2) | protein | 421 | 43% helix, 18% strand | D0VX29 |
| C | Cytochrome B | protein | 380 | 69% helix, 2% strand | P18946 |
| D, Q | Mitochondrial cytochrome C1, heme protein (EC 1.10.2.2) | protein | 241 | 40% helix, 8% strand | D0VX26 |
| E, R | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 196 | 22% helix, 17% strand | Q5ZLR5 |
| F, S | Cytochrome B-C1 complex subunit 7 | protein | 101 | 66% helix, 0% strand | D0VX30 |
| G | Mitochondrial ubiquinol-cytochrome C reductase ubiquinone- binding protein qp-C (EC 1.10.2.2) | protein | 80 | 58% helix, 11% strand | D0VX32 |
| H, U | Cytochrome B-C1 complex subunit 6 | protein | 68 | 72% helix, 0% strand | D0VX28 |
| I | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 44 | 0% helix, 14% 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 | 46% helix, 19% strand | D0VX31 |
| O | Mitochondrial ubiquinol-cytochrome-C reductase complex core protein 2 (EC 1.10.2.2) | protein | 422 | 43% helix, 19% strand | D0VX29 |
| P | Cytochrome B | protein | 379 | 70% helix, 2% strand | P18946 |
| T | Mitochondrial ubiquinol-cytochrome C reductase ubiquinone- binding protein qp-C (EC 1.10.2.2) | protein | 79 | 58% helix, 11% strand | D0VX32 |
| V | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 41 | 0% helix, 15% 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 · 14 copies · chains A, C, E, F, G, D, P, R, J, N, S, T, Q, W
- 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
- Y52 · methyl (2E)-3-methoxy-2-(2-{[(5-methoxy-1,3-benzothiazol-2-yl)sulfanyl]methyl}phenyl)prop-2-enoate · ligand · 2 copies · chains C, P
- U10 · Ubiquinone-10 · 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
- BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains C, D, E, J, P, R, Q
- GOL · Glycerol · additive · 2 copies · chains C, D, P, Q
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains C, G
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 | 801 | 0.85 | 0.87 | 77 | HEM, GOL |
| 2 | 794 | 0.84 | 0.87 | 77 | HEM, GOL |
| 3 | 445 | 0.81 | 0.88 | 49 | HEM, U10 |
| 4 | 124 | 0.80 | 0.98 | 26 | empty |
| 5 | 420 | 0.80 | 0.88 | 54 | HEM, U10 |
Interfaces
55 interfaces between chains.
- A–B · 2060 Ų buried · 32 hydrogen bonds · protein-protein
- N–O · 2054 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1678 Ų buried · 11 hydrogen bonds · protein-protein
- O–V · 1675 Ų buried · 16 hydrogen bonds · protein-protein
- P–Q · 1656 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 1 modified (heme c attachment, formylation).
Compared structures
- 4U3F · Cytochrome bc1 complex from chicken with designed inhibitor 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 4U3F · PDBe 4U3F · UniProt D0VX31 · UniProt D0VX29 · UniProt P18946 · UniProt D0VX26 · UniProt Q5ZLR5 · UniProt D0VX30 · UniProt D0VX32 · UniProt D0VX28 · UniProt D0VX27
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