Research workbench
Tubulin-RB3_SLD-TTL in complex with compound 5l
Analyse Tubulin-RB3_SLD-TTL in complex with compound 5l in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X1E
- Type
- protein
- Length
- 2,173 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Gallus gallus; Rattus norvegicus; Sus scrofa
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Stathmin-4; Tubulin Tyrosine Ligase
- UniProt
- Q2XVP4, A0A287AGU7, P63043, E1BQ43
- Ligands
- GTP, Y5L, GDP, ACP, MG, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.9 · 6 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 46% helix, 18% strand | Q2XVP4 |
| B | Tubulin beta-2B chain | protein | 427 | 47% helix, 19% strand | A0A287AGU7 |
| C | Tubulin alpha-1B chain | protein | 440 | 46% helix, 18% strand | Q2XVP4 |
| D | Tubulin beta-2B chain | protein | 421 | 49% helix, 19% strand | A0A287AGU7 |
| E | Stathmin-4 | protein | 121 | 78% helix, 13% strand | P63043 |
| F | Tubulin Tyrosine Ligase | protein | 327 | 31% helix, 24% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
- Y5L · 4-(2-chloro-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl)-7-methoxy-3,4-dihydroquinoxalin-2(1H)-one · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
- CA · Calcium ion · metal · 2 copies · chains A, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.86 | 0.95 | 61 | GTP, MG, Y5L |
| 2 | 957 | 0.86 | 0.87 | 120 | GTP, MG, Y5L |
| 3 | 1189 | 0.83 | 0.84 | 122 | GDP, MG |
| 4 | 180 | 0.76 | 0.92 | 34 | empty |
| 5 | 721 | 0.74 | 0.80 | 85 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1648 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1512 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1346 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 881 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 839 Ų buried · 7 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 Q2XVP4
- Every structure of UniProt A0A287AGU7
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 6X1E · PDBe 6X1E · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt P63043 · UniProt E1BQ43
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.