Research workbench
Tubulin-colchicine-soblidotin: stathmin-like domain complex
Analyse Tubulin-colchicine-soblidotin: 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
- 3E22
- Type
- protein
- Length
- 1,810 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1C chain; Tubulin beta-2B chain; Stathmin-4
- UniProt
- Q3ZCJ7, Q6B856, P63043
- Ligands
- GTP, GDP, LOC, TZT, MG
- Pockets
- 18 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1C chain | protein | 427 | 42% helix, 15% strand | Q3ZCJ7 |
| B, D | Tubulin beta-2B chain | protein | 419 | 44% helix, 16% strand | Q6B856 |
| C | Tubulin alpha-1C chain | protein | 421 | 40% helix, 14% strand | Q3ZCJ7 |
| E | Stathmin-4 | protein | 124 | 38% helix, 6% 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
- LOC · N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide · ligand · 2 copies · chains A, B, C, D
- TZT · Soblidotin · ligand · chains B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.84 | 0.85 | 111 | GTP, MG, LOC |
| 2 | 957 | 0.83 | 0.85 | 126 | GDP, TZT |
| 3 | 1101 | 0.83 | 0.84 | 115 | GTP, MG, LOC |
| 4 | 766 | 0.72 | 0.78 | 53 | empty |
| 5 | 469 | 0.69 | 0.80 | 37 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1577 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1330 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1286 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 872 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 739 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 Q3ZCJ7
- Every structure of UniProt Q6B856
- Every structure of UniProt P63043
- Elsewhere: RCSB PDB 3E22 · PDBe 3E22 · UniProt Q3ZCJ7 · UniProt Q6B856 · UniProt P63043
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