Research workbench
Cryo-EM structure of GDP-microtubule co-polymerised with doublecortin
Analyse Cryo-EM structure of GDP-microtubule co-polymerised with doublecortin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EVZ
- Type
- protein
- Length
- 5,166 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin beta chain; Tubulin alpha-1B chain
- UniProt
- P02554, Q2XVP4
- Ligands
- GDP, GTP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, G, D, I, B, H | Tubulin beta chain | protein | 429 | 39% helix, 17% strand | P02554 |
| A, E, J, C, L, K | Tubulin alpha-1B chain | protein | 432 | 39% helix, 16% strand | Q2XVP4 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains F, E, G, D, C, I, A, B, H
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains A, H, G, E, F, J, I, C, D, L, B, K
- MG · Magnesium ion · metal · 6 copies · chains A, E, F, J, C, D, L, B, 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 | 335 | 0.85 | 0.94 | 50 | GDP |
| 2 | 346 | 0.84 | 0.94 | 55 | GDP |
| 3 | 311 | 0.84 | 0.95 | 43 | GTP, MG |
| 4 | 299 | 0.84 | 0.95 | 43 | GTP, MG |
| 5 | 337 | 0.84 | 0.94 | 52 | GDP |
Interfaces
17 interfaces between chains.
- I–C · 1974 Ų buried · 24 hydrogen bonds · protein-protein
- F–J · 1952 Ų buried · 20 hydrogen bonds · protein-protein
- G–E · 1951 Ų buried · 21 hydrogen bonds · protein-protein
- D–L · 1950 Ų buried · 21 hydrogen bonds · protein-protein
- F–E · 1945 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6EVZ · Cryo-EM structure of GDP-microtubule co-polymerised with doublecortin · the same entry in another collection · chain F against F, 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 P02554
- Every structure of UniProt Q2XVP4
- Elsewhere: RCSB PDB 6EVZ · PDBe 6EVZ · UniProt P02554 · UniProt Q2XVP4
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