Research workbench
Tubulin-spongistatin complex
Analyse Tubulin-spongistatin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FII
- Type
- protein
- Length
- 2,197 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Stathmin-4; Tubulin tyrosine ligase
- UniProt
- P81947, Q6B856, P63043, E1BQ43
- Ligands
- GTP, GDP, SG9, ACP, MG, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 438 | 47% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 424 | 48% helix, 20% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 440 | 47% helix, 17% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 423 | 49% helix, 20% strand | Q6B856 |
| E | Stathmin-4 | protein | 123 | 77% helix, 14% strand | P63043 |
| F | Tubulin tyrosine ligase | protein | 349 | 31% helix, 22% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
- SG9 · Spongistatin-1 · ligand · chains D
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains B, A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 870 | 0.84 | 0.86 | 109 | GDP, MG, GOL, DMS |
| 2 | 1161 | 0.79 | 0.81 | 112 | GTP, MG |
| 3 | 1200 | 0.79 | 0.81 | 110 | ACP, MG |
| 4 | 552 | 0.78 | 0.85 | 62 | GTP, MG |
| 5 | 212 | 0.78 | 0.92 | 29 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1587 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1419 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1328 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 945 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 812 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6FII · Tubulin-Spongistatin 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 P81947
- Every structure of UniProt Q6B856
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 6FII · PDBe 6FII · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.