Research workbench
TUBULIN:F3II darpin complex
Analyse TUBULIN:F3II darpin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GVM
- Type
- protein
- Length
- 1,077 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain; Stathmin-like domain R1; F3II darpin
- UniProt
- D0VWZ0, D0VWY9
- Ligands
- GTP, GDP, MG
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 428 | 47% helix, 18% strand | D0VWZ0 |
| B | Tubulin beta chain | protein | 425 | 50% helix, 20% strand | D0VWY9 |
| C | Stathmin-like domain R1 | protein | 65 | 52% helix, 20% strand | — |
| D | F3II darpin | protein | 159 | 56% helix, 0% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · 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
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.74 | 0.86 | 53 | GTP, MG |
| 2 | 556 | 0.70 | 0.79 | 49 | empty |
| 3 | 345 | 0.68 | 0.81 | 43 | empty |
| 4 | 188 | 0.64 | 0.85 | 34 | GDP |
| 5 | 149 | 0.57 | 0.82 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1501 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1445 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 690 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 612 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 45 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6GVM · Tubulin:F3II DARPin 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 6GVM · PDBe 6GVM · UniProt D0VWZ0 · UniProt D0VWY9
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