Research workbench
AVAR1 bound to avenolide
Analyse AVAR1 bound to avenolide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WP9
- Type
- protein
- Length
- 1,716 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AVAR1
- UniProt
- Q82H41
- Ligands
- XVR
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 7 distinct chains · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AVAR1 | protein | 211 | 71% helix, 1% strand | Q82H41 |
| B | AVAR1 | protein | 216 | 71% helix, 1% strand | Q82H41 |
| C | AVAR1 | protein | 213 | 69% helix, 1% strand | Q82H41 |
| D | AVAR1 | protein | 216 | 71% helix, 1% strand | Q82H41 |
| E | AVAR1 | protein | 218 | 70% helix, 1% strand | Q82H41 |
| F, G | AVAR1 | protein | 215 | 72% helix, 1% strand | Q82H41 |
| H | AVAR1 | protein | 212 | 69% helix, 1% strand | Q82H41 |
Ligands and binding sites
- XVR · (5S)-5-[(6R)-6-hydroxy-6-methyl-5-oxooctyl]furan-2(5H)-one · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.80 | 0.81 | 79 | empty |
| 2 | 112 | 0.79 | 0.98 | 22 | XVR |
| 3 | 103 | 0.79 | 0.98 | 23 | XVR |
| 4 | 116 | 0.79 | 0.97 | 23 | XVR |
| 5 | 1142 | 0.78 | 0.80 | 90 | empty |
Interfaces
13 interfaces between chains.
- D–H · 1669 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 1632 Ų buried · 23 hydrogen bonds · protein-protein
- C–G · 808 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 787 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 435 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6WP9 · AvaR1 bound to Avenolide · the same entry in another collection · chain A against A, 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 Q82H41
- Elsewhere: RCSB PDB 6WP9 · PDBe 6WP9 · UniProt Q82H41
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