Research workbench
Cryo-EM structure of GDP-microtubule co-polymerised with doublecortin and supplemented with taxol
Analyse Cryo-EM structure of GDP-microtubule co-polymerised with doublecortin and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EW0
- Type
- protein
- Length
- 5,166 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain
- UniProt
- Q2XVP4, P02554
- Ligands
- GTP, GDP, TA1, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, J, C, L, A, K | Tubulin alpha-1B chain | protein | 432 | 43% helix, 15% strand | Q2XVP4 |
| F, G, D, I, B, H | Tubulin beta chain | protein | 429 | 44% helix, 16% strand | P02554 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains E, G, F, J, C, I, L, D, A, H, K, B
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains E, F, G, C, D, I, A, B, H
- TA1 · Taxol · ligand · 6 copies · chains F, G, D, I, B, H
- MG · Magnesium ion · metal · 6 copies · chains E, F, J, C, L, A, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.84 | 0.95 | 45 | GTP, MG |
| 2 | 339 | 0.84 | 0.94 | 48 | GDP |
| 3 | 313 | 0.84 | 0.94 | 46 | GTP, MG |
| 4 | 341 | 0.84 | 0.94 | 44 | GDP |
| 5 | 301 | 0.83 | 0.94 | 42 | GTP, MG |
Interfaces
17 interfaces between chains.
- C–D · 1930 Ų buried · 17 hydrogen bonds · protein-protein
- L–D · 1922 Ų buried · 21 hydrogen bonds · protein-protein
- A–H · 1921 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1917 Ų buried · 16 hydrogen bonds · protein-protein
- C–I · 1916 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6EW0 · Cryo-EM structure of GDP-microtubule co-polymerised with doublecortin and supplemented… · the same entry in another collection · chain E against E, TM-score 1.00
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 Q2XVP4
- Every structure of UniProt P02554
- Elsewhere: RCSB PDB 6EW0 · PDBe 6EW0 · UniProt Q2XVP4 · UniProt P02554
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