Research workbench
TUBULIN:IIH5 alpharep complex
Analyse TUBULIN:IIH5 alpharep complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GWD
- Type
- protein
- Length
- 3,056 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-tubulin; Tubulin beta chain; IIH5 alpharep
- UniProt
- D0VWY9
- Ligands
- GTP, GDP, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 9 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-tubulin | protein | 434 | 44% helix, 18% strand | — |
| B | Tubulin beta chain | protein | 430 | 48% helix, 19% strand | D0VWY9 |
| C | Alpha-tubulin | protein | 436 | 44% helix, 18% strand | — |
| D | Tubulin beta chain | protein | 430 | 48% helix, 19% strand | D0VWY9 |
| E | Alpha-tubulin | protein | 432 | 45% helix, 18% strand | — |
| F | Tubulin beta chain | protein | 431 | 47% helix, 18% strand | D0VWY9 |
| G | IIH5 alpharep | protein | 153 | 72% helix, 0% strand | — |
| H | IIH5 alpharep | protein | 156 | 74% helix, 0% strand | — |
| I | IIH5 alpharep | protein | 154 | 75% helix, 0% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D, E, F
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains B, D, F
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, E, F
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 | 165 | 0.79 | 0.95 | 34 | GTP, MG |
| 2 | 513 | 0.78 | 0.86 | 62 | GTP, MG |
| 3 | 474 | 0.78 | 0.86 | 55 | GTP, MG |
| 4 | 471 | 0.68 | 0.79 | 45 | empty |
| 5 | 505 | 0.67 | 0.78 | 48 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1446 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1431 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1385 Ų buried · 19 hydrogen bonds · protein-protein
- A–G · 856 Ų buried · 7 hydrogen bonds · protein-protein
- E–I · 828 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6GWD · Tubulin:iiH5 alphaRep 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 D0VWY9
- Elsewhere: RCSB PDB 6GWD · PDBe 6GWD · UniProt D0VWY9
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