MolNFT v1 · #137927 · protein
Yeast microtubule stabilized with taxol assembled from mutated tubulin
5W3J · Tubulin alpha-1 chain: “Yeast microtubule stabilized with taxol assembled from mutated tubulin”. Electron microscopy, 4 ligands (GTP, GDP, TA1), 12 pockets (best druggability 0.83). MolNFT v1 #137927 on GenesisL1: 3D structure…
- PDB
- 5W3J
- 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, TA1, MG
- Pockets
- 12 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1 chain | protein | 440 | 40% helix, 13% strand | P09733 |
| B | Tubulin beta chain | protein | 427 | 38% helix, 16% strand | P02557 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- TA1 · Taxol · 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
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.83 | 0.93 | 45 | GTP, MG |
| 2 | 380 | 0.65 | 0.79 | 47 | GDP |
| 3 | 361 | 0.62 | 0.78 | 33 | TA1 |
| 4 | 67 | 0.55 | 0.87 | 23 | empty |
| 5 | 261 | 0.55 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1939 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5W3J · Yeast microtubule stabilized with Taxol assembled from mutated tubulin · 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 0.97
- P02557 · AlphaFold monomer V2.0 prediction for tubulin beta chain (P02557) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 5W3J · PDBe 5W3J · UniProt P09733 · UniProt P02557
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