Research workbench
Cytochrome BC1 bound to the 4(1H)-pyridone GSK932121
Analyse Cytochrome BC1 bound to the 4(1H)-pyridone GSK932121 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D6U
- Type
- protein
- Length
- 3,866 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, G8U, HEC, FES, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 20 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome B-C1 complex subunit 1, mitochondrial | protein | 444 | 45% helix, 18% strand | P31800 |
| B | Cytochrome B-C1 complex subunit 2, mitochondrial | protein | 422 | 43% helix, 19% strand | P23004 |
| C | Cytochrome B | protein | 374 | 72% helix, 2% strand | P00157 |
| D | Cytochrome C1, heme protein, mitochondrial | protein | 240 | 41% helix, 8% strand | P00125 |
| E | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 73 | 62% helix, 1% strand | P13272 |
| F | Cytochrome B-C1 complex subunit 7 | protein | 98 | 69% helix, 1% strand | P00129 |
| G | Cytochrome B-C1 complex subunit 8 | protein | 80 | 53% helix, 9% strand | P13271 |
| H | Cytochrome B-C1 complex subunit 6, mitochondrial | protein | 65 | 75% helix, 0% strand | P00126 |
| I | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 27 | 0% helix, 30% strand | P13272 |
| J | Cytochrome B-C1 complex subunit 9 | protein | 58 | 74% helix, 0% strand | P00130 |
| N | Cytochrome B-C1 complex subunit 1, mitochondrial | protein | 444 | 44% helix, 19% strand | P31800 |
| O | Cytochrome B-C1 complex subunit 2, mitochondrial | protein | 419 | 43% helix, 19% strand | P23004 |
| P | Cytochrome B | protein | 370 | 73% 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 (EC 1.10.2.2) | protein | 196 | 29% helix, 16% strand | P13272 |
| S | Cytochrome B-C1 complex subunit 7 | protein | 99 | 69% helix, 1% strand | P00129 |
| T | Cytochrome B-C1 complex subunit 8 | protein | 74 | 57% helix, 9% strand | P13271 |
| U | Cytochrome B-C1 complex subunit 6, mitochondrial | protein | 66 | 70% helix, 0% strand | P00126 |
| V | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 17 | 0% helix, 47% 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
- G8U · 3-chloro-6-(hydroxymethyl)-2-methyl-5-{4-[3-(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 · 9 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 | 449 | 0.85 | 0.92 | 47 | HEM |
| 2 | 881 | 0.83 | 0.84 | 89 | HEM |
| 3 | 1166 | 0.82 | 0.83 | 124 | PO4, PEE |
| 4 | 1121 | 0.82 | 0.82 | 92 | PEE, CDL |
| 5 | 1000 | 0.81 | 0.82 | 71 | empty |
Interfaces
54 interfaces between chains.
- A–B · 2247 Ų buried · 39 hydrogen bonds · protein-protein
- N–O · 2147 Ų buried · 40 hydrogen bonds · protein-protein
- P–Q · 1677 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1669 Ų buried · 20 hydrogen bonds · protein-protein
- C–P · 1272 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 4D6U · Cytochrome bc1 bound to the 4(1H)-pyridone GSK932121 · 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 4D6U · PDBe 4D6U · UniProt P31800 · UniProt P23004 · UniProt P00157 · UniProt P00125 · UniProt P13272 · UniProt P00129 · UniProt P13271 · UniProt P00126 · UniProt P00130
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