Research workbench
Tubulin-inhibitor complex
Analyse Tubulin-inhibitor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TDE
- Type
- protein
- Length
- 1,858 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain; Stathmin-4
- UniProt
- P63043
- Ligands
- GTP, GDP, N3Z, MG, SO4
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tubulin alpha chain | protein | 434 | 46% helix, 18% strand | — |
| B | Tubulin beta chain | protein | 430 | 49% helix, 18% strand | — |
| D | Tubulin beta chain | protein | 429 | 49% helix, 18% strand | — |
| E | Stathmin-4 | protein | 131 | 72% helix, 13% strand | P63043 |
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
- N3Z · ~{N}-[(10~{S})-3,4,5-trimethoxy-16-methylidene-14-oxatetracyclo[9.7.0.0^{2,7}.0^{13,17}]octadeca-1(18), 2,4,6,11,13(17)-hexaen-10-yl]ethanamide · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.84 | 0.86 | 100 | GTP, MG, N3Z |
| 2 | 1143 | 0.82 | 0.83 | 104 | GTP, MG, N3Z |
| 3 | 680 | 0.80 | 0.85 | 85 | GDP |
| 4 | 656 | 0.71 | 0.78 | 52 | empty |
| 5 | 140 | 0.67 | 0.89 | 33 | GDP |
Interfaces
7 interfaces between chains.
- A–E · 1871 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 1377 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1375 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1305 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 828 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6TDE · Tubulin-inhibitor 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 P63043
- Elsewhere: RCSB PDB 6TDE · PDBe 6TDE · UniProt P63043
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