Research workbench
TUBULIN:STATHMIN-like domain complex
Analyse TUBULIN:STATHMIN-like domain complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F61
- Type
- protein
- Length
- 3,685 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain; Stathmin-like domain R4
- UniProt
- D0VWZ0, D0VWY9
- Ligands
- GTP, GDP, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 431 | 46% helix, 18% strand | D0VWZ0 |
| B, D, F | Tubulin beta chain | protein | 432 | 48% helix, 19% strand | D0VWY9 |
| C, E, G | Tubulin alpha chain | protein | 431 | 46% helix, 17% strand | D0VWZ0 |
| H | Tubulin beta chain | protein | 431 | 48% helix, 19% strand | D0VWY9 |
| I | Stathmin-like domain R4 | protein | 234 | 78% helix, 6% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains B, D, F, H
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D, E, F, G, H
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 | 830 | 0.80 | 0.83 | 99 | GDP |
| 2 | 898 | 0.80 | 0.82 | 108 | GDP |
| 3 | 1056 | 0.80 | 0.81 | 110 | GTP, MG |
| 4 | 1087 | 0.80 | 0.81 | 107 | GTP, MG |
| 5 | 806 | 0.79 | 0.83 | 92 | GDP |
Interfaces
15 interfaces between chains.
- A–I · 1891 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1554 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1545 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1513 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1409 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4F61 · Tubulin:Stathmin-like domain complex · the same entry in another collection · chain A against A, 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 D0VWZ0
- Every structure of UniProt D0VWY9
- Elsewhere: RCSB PDB 4F61 · PDBe 4F61 · UniProt D0VWZ0 · UniProt D0VWY9
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