MolNFT v2 · #217758 · protein
Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution: 96 fs structure
8QEA · Tubulin alpha-1B chain: “Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution: 96 fs structure”. X-ray diffraction at 1.8, 4 ligands (GTP, IBL, MG), 11 pockets (best druggability 0.79). MolNFT v2…
- PDB
- 8QEA
- Type
- protein
- Length
- 1,017 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, IBL, MG, CA
- Pockets
- 11 · best druggability 0.79
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 | 436 | 45% helix, 17% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 426 | 48% helix, 19% strand | Q6B856 |
| F | Designed Ankyrin Repeat Protein (DARPIN) D1 | protein | 155 | 54% helix, 0% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- IBL · Azo-Combretastatin A4 (cis) · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.79 | 0.85 | 66 | IBL |
| 2 | 290 | 0.76 | 0.89 | 43 | GTP, MG |
| 3 | 363 | 0.61 | 0.78 | 45 | empty |
| 4 | 165 | 0.58 | 0.82 | 31 | GTP |
| 5 | 56 | 0.54 | 0.89 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1458 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 944 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- P81947 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (P81947) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 8QEA · PDBe 8QEA · UniProt P81947 · UniProt Q6B856
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