Research workbench
Tubulin-RB3_SLD-TTL in complex with compound DJ95
Analyse Tubulin-RB3_SLD-TTL in complex with compound DJ95 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NNG
- Type
- protein
- Length
- 2,187 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.397
- Source
- Gallus gallus; Homo sapiens; Sus scrofa
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Stathmin-4; Tubulin Tyrosine Ligase
- UniProt
- Q2XVP4, A0A287AGU7, Q9H169, E1BQ43
- Ligands
- GTP, GDP, DJ9, ACP, MG, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.397 · 6 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 439 | 46% helix, 18% strand | Q2XVP4 |
| B | Tubulin beta-2B chain | protein | 427 | 49% helix, 19% strand | A0A287AGU7 |
| C | Tubulin alpha-1B chain | protein | 440 | 47% helix, 17% strand | Q2XVP4 |
| D | Tubulin beta-2B chain | protein | 421 | 48% helix, 19% strand | A0A287AGU7 |
| E | Stathmin-4 | protein | 121 | 77% helix, 14% strand | Q9H169 |
| F | Tubulin Tyrosine Ligase | protein | 339 | 32% helix, 20% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- DJ9 · 2-(1H-indol-6-yl)-4-(3,4,5-trimethoxyphenyl)-1H-imidazo[4,5-c]pyridine · ligand · chains A, B
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 4 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.86 | 0.87 | 128 | GTP, MG, DJ9 |
| 2 | 1006 | 0.85 | 0.86 | 123 | GDP, MG |
| 3 | 420 | 0.77 | 0.86 | 55 | GTP, MG |
| 4 | 131 | 0.76 | 0.95 | 30 | empty |
| 5 | 880 | 0.73 | 0.77 | 71 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1590 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1399 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1249 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 874 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 868 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6NNG · Tubulin-RB3_SLD-ttl in complex with compound DJ95 · the same entry in another collection · chain F against F, TM-score 1.00
- Q2XVP4 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (Q2XVP4) · a predicted model of the same protein · chain C against A, TM-score 0.96
- Q9H169 · AlphaFold monomer V2.0 prediction for stathmin-4 (Q9H169) · a predicted model of the same protein · chain E against A, TM-score 0.76
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 Q9H169
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 6NNG · PDBe 6NNG · UniProt Q2XVP4 · UniProt A0A287AGU7 · UniProt Q9H169 · UniProt E1BQ43
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