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Crystal structures of flap bound to mk-866
Analyse Crystal structures of flap bound to mk-866 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VGI
- Type
- protein
- Length
- 870 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-lipoxygenase-activating protein
- UniProt
- P20292
- Ligands
- QY7, SO4
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-lipoxygenase-activating protein | protein | 139 | 87% helix, 0% strand | P20292 |
| B | 5-lipoxygenase-activating protein | protein | 140 | 85% helix, 0% strand | P20292 |
| C | 5-lipoxygenase-activating protein | protein | 143 | 81% helix, 0% strand | P20292 |
| D | 5-lipoxygenase-activating protein | protein | 150 | 82% helix, 0% strand | P20292 |
| E | 5-lipoxygenase-activating protein | protein | 144 | 81% helix, 0% strand | P20292 |
| F | 5-lipoxygenase-activating protein | protein | 154 | 78% helix, 0% strand | P20292 |
Ligands and binding sites
- QY7 · 3-[3-(tert-butylsulfanyl)-1-[(4-chlorophenyl)methyl]-5-(propan-2-yl)-1H-indol-2-yl]-2,2-dimethylpropanoic acid · ligand · 6 copies · chains A, F, B, C, D, E
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.86 | 0.90 | 58 | empty |
| 2 | 577 | 0.85 | 0.90 | 41 | empty |
| 3 | 242 | 0.73 | 0.88 | 41 | empty |
| 4 | 304 | 0.72 | 0.86 | 38 | empty |
| 5 | 315 | 0.72 | 0.85 | 42 | empty |
Interfaces
15 interfaces between chains.
- E–F · 1448 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1382 Ų buried · 14 hydrogen bonds · protein-protein
- A–F · 1170 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1130 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1128 Ų buried · 10 hydrogen bonds · protein-protein
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 P20292
- Elsewhere: RCSB PDB 6VGI · PDBe 6VGI · UniProt P20292
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