Research workbench
Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes
Analyse Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S8K
- Type
- protein
- Length
- 1,017 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.52
- 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, PN6, GDP, MG
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.52 · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 46% helix, 17% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 425 | 50% 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 · chains A, B
- PN6 · (3Z,6Z)-3-benzylidene-6-[(5-tert-butyl-1H-imidazol-4-yl)methylidene]piperazine-2,5-dione · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.84 | 0.85 | 112 | GTP, MG, PN6 |
| 2 | 200 | 0.63 | 0.83 | 34 | GDP |
| 3 | 376 | 0.62 | 0.78 | 46 | empty |
| 4 | 55 | 0.54 | 0.89 | 19 | empty |
| 5 | 114 | 0.49 | 0.80 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1467 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 912 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6S8K · Structure, thermodynamics, and kinetics of plinabulin binding to two tubulin isotypes · the same entry in another collection · chain A against A, TM-score 1.00
- 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 6S8K · PDBe 6S8K · UniProt P81947 · UniProt Q6B856
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