MolNFT v1 · #167293 · protein
Crystal structures of flap bound to dg-031
6VGC · 5-lipoxygenase-activating protein: “Crystal structures of flap bound to dg-031”. X-ray diffraction, 2 ligands (QY1, CA), 16 pockets (best druggability 0.85). MolNFT v1 #167293 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6VGC
- Type
- protein
- Length
- 901 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-lipoxygenase-activating protein
- UniProt
- P20292
- Ligands
- QY1, CA
- Pockets
- 16 · best druggability 0.85
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 | 144 | 83% helix, 0% strand | P20292 |
| B | 5-lipoxygenase-activating protein | protein | 149 | 82% helix, 0% strand | P20292 |
| C | 5-lipoxygenase-activating protein | protein | 151 | 79% helix, 0% strand | P20292 |
| D | 5-lipoxygenase-activating protein | protein | 155 | 81% helix, 0% strand | P20292 |
| E | 5-lipoxygenase-activating protein | protein | 154 | 84% helix, 0% strand | P20292 |
| F | 5-lipoxygenase-activating protein | protein | 148 | 84% helix, 0% strand | P20292 |
Ligands and binding sites
- QY1 · (2R)-cyclopentyl{4-[(quinolin-2-yl) methoxy]phenyl}acetic acid · ligand · 6 copies · chains A, C, B, F, D, E
- CA · Calcium ion · metal · 2 copies · chains A, B, C, D, E, F
- BOG · octyl beta-D-glucopyranoside · additive · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.85 | 0.90 | 50 | empty |
| 2 | 541 | 0.84 | 0.89 | 41 | empty |
| 3 | 392 | 0.75 | 0.85 | 42 | empty |
| 4 | 212 | 0.74 | 0.89 | 31 | QY1 |
| 5 | 259 | 0.73 | 0.87 | 39 | empty |
Interfaces
15 interfaces between chains.
- B–C · 1405 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1372 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 1364 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 1336 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1238 Ų buried · 12 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 6VGC · PDBe 6VGC · UniProt P20292
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