Research workbench
Tubulin-RB3_SLD in complex with colchicine
Analyse Tubulin-RB3_SLD in complex with colchicine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XER
- Type
- protein
- Length
- 1,827 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta chain; Stathmin-4
- UniProt
- Q2XVP4, A0A287AGU7, P63043
- Ligands
- GTP, LOC, GDP, MG, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 426 | 47% helix, 18% strand | Q2XVP4 |
| B | Tubulin beta chain | protein | 425 | 49% helix, 19% strand | A0A287AGU7 |
| C | Tubulin alpha-1B chain | protein | 426 | 47% helix, 18% strand | Q2XVP4 |
| D | Tubulin beta chain | protein | 430 | 48% helix, 19% strand | A0A287AGU7 |
| E | Stathmin-4 | protein | 120 | 78% helix, 13% strand | P63043 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, 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
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.84 | 0.87 | 92 | GTP, MG, LOC |
| 2 | 922 | 0.83 | 0.85 | 97 | GTP, MG, LOC |
| 3 | 746 | 0.80 | 0.84 | 87 | GDP |
| 4 | 653 | 0.68 | 0.77 | 67 | empty |
| 5 | 301 | 0.68 | 0.83 | 28 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1632 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1438 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1352 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1327 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 807 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6XER · Tubulin-RB3_SLD in complex with colchicine · 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 Q2XVP4
- Every structure of UniProt A0A287AGU7
- Every structure of UniProt P63043
- Elsewhere: RCSB PDB 6XER · PDBe 6XER · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63043
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