Research workbench
The binding mode of epothilone a on A,B-tubulin by electron crystallography
Analyse The binding mode of epothilone a on A,B-tubulin by electron crystallography in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TVK
- Type
- protein
- Length
- 838 residues
- Chains
- 2
- Method
- electron crystallography
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain
- UniProt
- P02550, P02554
- Ligands
- GTP, GDP, EP
- Pockets
- 12 · best druggability 0.83
Structure
electron crystallography · 2 distinct chains · 37% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 412 | 37% helix, 11% strand | P02550 |
| B | Tubulin beta chain | protein | 426 | 36% helix, 12% strand | P02554 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- EP · Epothilone A · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.83 | 0.96 | 44 | GTP |
| 2 | 70 | 0.71 | 0.96 | 24 | empty |
| 3 | 270 | 0.65 | 0.82 | 45 | empty |
| 4 | 273 | 0.62 | 0.80 | 26 | empty |
| 5 | 319 | 0.61 | 0.78 | 27 | EP |
Interfaces
1 interface between chains.
- A–B · 1825 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1TVK · The binding mode of epothilone A on a,b-tubulin by electron crystallography · the same entry in another collection · chain A against A, TM-score 1.00
- P02550 · AlphaFold monomer V2.0 prediction for tubulin alpha-1A chain (P02550) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P02550
- Every structure of UniProt P02554
- Elsewhere: RCSB PDB 1TVK · PDBe 1TVK · UniProt P02550 · UniProt P02554
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