Research workbench
Tubulin-RB3_SLD in complex with compound 40A
Analyse Tubulin-RB3_SLD in complex with compound 40A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XES
- Type
- protein
- Length
- 1,835 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, TU3, GDP, MG, SO4
- Pockets
- 20 · best druggability 0.86
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 | 427 | 48% helix, 18% strand | Q2XVP4 |
| B | Tubulin beta chain | protein | 425 | 50% helix, 19% strand | A0A287AGU7 |
| C | Tubulin alpha-1B chain | protein | 427 | 46% helix, 18% strand | Q2XVP4 |
| D | Tubulin beta chain | protein | 431 | 48% helix, 19% strand | A0A287AGU7 |
| E | Stathmin-4 | protein | 125 | 74% helix, 14% strand | P63043 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
- TU3 · [6-(3-hydroxy-4-methylphenyl)pyrazin-2-yl](3,4,5-trimethoxyphenyl)methanone · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · chains C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, D
- DMS · Dimethyl sulfoxide · additive · chains 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 426 | 0.86 | 0.93 | 63 | GTP, TU3 |
| 2 | 987 | 0.85 | 0.86 | 96 | GTP, MG, TU3 |
| 3 | 823 | 0.82 | 0.84 | 103 | GDP |
| 4 | 439 | 0.70 | 0.81 | 43 | empty |
| 5 | 631 | 0.70 | 0.78 | 67 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1801 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1428 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1391 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1340 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 848 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6XES · Tubulin-RB3_SLD in complex with compound 40a · 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 6XES · PDBe 6XES · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63043
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