Research workbench
Yeast microtubule stabilized with epothilone
Analyse Yeast microtubule stabilized with epothilone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W3H
- Type
- protein
- Length
- 867 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1 chain; Tubulin beta chain
- UniProt
- P09733, P02557
- Ligands
- GTP, GDP, EP, MG
- Pockets
- 10 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1 chain | protein | 440 | 49% helix, 18% strand | P09733 |
| B | Tubulin beta chain | protein | 427 | 50% helix, 19% strand | P02557 |
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
- MG · Magnesium 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.82 | 0.92 | 50 | GTP, MG |
| 2 | 262 | 0.62 | 0.80 | 42 | GDP |
| 3 | 319 | 0.55 | 0.75 | 37 | EP |
| 4 | 175 | 0.47 | 0.76 | 22 | empty |
| 5 | 142 | 0.43 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1837 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5W3H · Yeast microtubule stabilized with epothilone · the same entry in another collection · chain A against A, TM-score 1.00
- P09733 · AlphaFold monomer V2.0 prediction for tubulin alpha-1 chain (P09733) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P02557 · AlphaFold monomer V2.0 prediction for tubulin beta chain (P02557) · a predicted model of the same protein · chain B 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 P09733
- Every structure of UniProt P02557
- Elsewhere: RCSB PDB 5W3H · PDBe 5W3H · UniProt P09733 · UniProt P02557
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