MolNFT v1 · #88823 · protein
Cytochrome BC1 bound to the 4(1H)-pyridone GW844520
4D6T · Cytochrome B-C1 complex subunit 1, mitochondrial: “Cytochrome BC1 bound to the 4(1H)-pyridone GW844520”. X-ray diffraction, 7 ligands (HEM, PEE, CDL), 20 pockets (best druggability 0.86). MolNFT v1 #88823 on GenesisL1: 3D structure…
- PDB
- 4D6T
- Type
- protein
- Length
- 3,860 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome B-C1 complex subunit 1, mitochondrial; Cytochrome B-C1 complex subunit 2…
- EC
- 1.10.2.2
- UniProt
- P31800, P23004, P00157, P00125, P13272, P00129, P13271, P00126, P00130
- Ligands
- HEM, PEE, CDL, 4X9, HEC, FES, PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 19 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, N | Cytochrome B-C1 complex subunit 1, mitochondrial | protein | 444 | 44% helix, 18% strand | P31800 |
| B | Cytochrome B-C1 complex subunit 2, mitochondrial | protein | 422 | 42% helix, 19% strand | P23004 |
| C | Cytochrome B | protein | 374 | 70% helix, 2% strand | P00157 |
| D | Cytochrome C1, heme protein, mitochondrial | protein | 240 | 40% helix, 8% strand | P00125 |
| E | Cytochrome B-C1 complex subunit rieske, mitochondrial | protein | 73 | 62% helix, 1% strand | P13272 |
| F | Cytochrome B-C1 complex subunit 7 | protein | 98 | 72% helix, 1% strand | P00129 |
| G | Cytochrome B-C1 complex subunit 8 | protein | 80 | 53% helix, 11% strand | P13271 |
| H | Cytochrome B-C1 complex subunit 6, mitochondrial | protein | 65 | 77% helix, 0% strand | P00126 |
| I | Cytochrome B-C1 complex subunit rieske, mitochondrial | protein | 21 | 0% helix, 29% strand | P13272 |
| J | Cytochrome B-C1 complex subunit 9 | protein | 58 | 74% helix, 0% strand | P00130 |
| O | Cytochrome B-C1 complex subunit 2, mitochondrial | protein | 419 | 42% helix, 19% strand | P23004 |
| P | Cytochrome B | protein | 370 | 72% helix, 2% strand | P00157 |
| Q | Cytochrome C1, heme protein, mitochondrial | protein | 241 | 41% helix, 8% strand | P00125 |
| R | Cytochrome B-C1 complex subunit rieske, mitochondrial | protein | 196 | 29% helix, 14% strand | P13272 |
| S | Cytochrome B-C1 complex subunit 7 | protein | 99 | 73% helix, 1% strand | P00129 |
| T | Cytochrome B-C1 complex subunit 8 | protein | 74 | 55% helix, 9% strand | P13271 |
| U | Cytochrome B-C1 complex subunit 6, mitochondrial | protein | 66 | 74% helix, 0% strand | P00126 |
| V | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 17 | 0% helix, 41% strand | P13272 |
| W | Cytochrome B-C1 complex subunit 9 | protein | 59 | 73% helix, 0% strand | P00130 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, P
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 4 copies · chains C, F, G, D, E, J, P, S, T, Q, R, W
- CDL · Cardiolipin · ligand · 4 copies · chains C, D, F, G, P, Q, S, T
- 4X9 · 3-chloro-2,6-dimethyl-5-{4-[4-(trifluoromethoxy)phenoxy]phenyl}pyridin-4-ol · ligand · 2 copies · chains C, P
- HEC · Heme C · ligand · 2 copies · chains D, Q
- FES · Fe2/s2 (inorganic) cluster · ligand · chains R
- PO4 · Phosphate ion · ion · 11 copies · chains A, C, E, D, J, F, O, N, R, W, P, B, S
- GOL · Glycerol · additive · chains C, R
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 | 488 | 0.86 | 0.92 | 54 | HEM |
| 2 | 716 | 0.82 | 0.85 | 80 | PO4 |
| 3 | 910 | 0.81 | 0.83 | 83 | HEM |
| 4 | 796 | 0.81 | 0.83 | 70 | PEE |
| 5 | 925 | 0.80 | 0.82 | 80 | empty |
Interfaces
53 interfaces between chains.
- A–B · 2231 Ų buried · 41 hydrogen bonds · protein-protein
- N–O · 2128 Ų buried · 42 hydrogen bonds · protein-protein
- P–Q · 1667 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1660 Ų buried · 18 hydrogen bonds · protein-protein
- C–P · 1241 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4D6T · Cytochrome bc1 bound to the 4(1H)-pyridone GW844520 · 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 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
- Elsewhere: RCSB PDB 4D6T · PDBe 4D6T · UniProt P31800 · UniProt P23004 · UniProt P00157 · UniProt P00125 · UniProt P13272 · UniProt P00129 · UniProt P13271 · UniProt P00126 · UniProt P00130
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