Research workbench
Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution: 1 ns structure
Analyse Ultrafast structural transitions in an azobenzene photoswitch at near-atomic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8QL9
- Type
- protein
- Length
- 1,018 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Bos taurus; synthetic construct
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Designed Ankyrin Repeat Protein (DARPIN) D1
- UniProt
- P81947, Q6B856
- Ligands
- GTP, GDP, IBL, MG, CA
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · resolution 1.8 · 3 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 45% helix, 17% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 426 | 47% helix, 19% strand | Q6B856 |
| F | Designed Ankyrin Repeat Protein (DARPIN) D1 | protein | 155 | 53% helix, 0% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- IBL · Azo-Combretastatin A4 (cis) · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.85 | 0.86 | 101 | GTP, MG, IBL |
| 2 | 148 | 0.57 | 0.82 | 31 | GDP |
| 3 | 168 | 0.55 | 0.81 | 28 | empty |
| 4 | 219 | 0.54 | 0.78 | 23 | empty |
| 5 | 58 | 0.53 | 0.88 | 12 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1413 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 953 Ų buried · 13 hydrogen bonds · protein-protein
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 P81947
- Every structure of UniProt Q6B856
- Elsewhere: RCSB PDB 8QL9 · PDBe 8QL9 · UniProt P81947 · UniProt Q6B856
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.