MolNFT v1 · #111177 · protein
Crystal structure of tubulin bound to mi-181
4YJ2 · Tubulin alpha-1B chain: “Crystal structure of tubulin bound to mi-181”. X-ray diffraction, 5 ligands (GTP, GDP, 4ED), 20 pockets (best druggability 0.85). MolNFT v1 #111177 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4YJ2
- Type
- protein
- Length
- 2,137 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-2B chain; Stathmin-4; Tubulin-tyrosine ligase
- UniProt
- P81947, Q6B856, P63043, E1BQ43
- Ligands
- GTP, GDP, 4ED, MG, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 437 | 45% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 422 | 48% helix, 19% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 440 | 45% helix, 18% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 421 | 49% helix, 19% strand | Q6B856 |
| E | Stathmin-4 | protein | 121 | 76% helix, 14% strand | P63043 |
| F | Tubulin-tyrosine ligase | protein | 296 | 31% helix, 22% strand | E1BQ43 |
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
- 4ED · 5,6-dimethyl-2-[(E)-2-(pyridin-3-yl)ethenyl]-1,3-benzothiazole · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 5 copies · chains A, F, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
- IMD · Imidazole · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.85 | 0.86 | 125 | GTP, MG, 4ED |
| 2 | 1031 | 0.84 | 0.85 | 121 | GDP, MG, GOL |
| 3 | 971 | 0.83 | 0.84 | 119 | GTP, GOL, MG, 4ED |
| 4 | 146 | 0.76 | 0.94 | 28 | empty |
| 5 | 826 | 0.71 | 0.77 | 68 | GOL |
Interfaces
9 interfaces between chains.
- A–E · 1627 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1493 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1449 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 917 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 820 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4YJ2 · Crystal structure of tubulin bound to MI-181 · 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 P81947
- Every structure of UniProt Q6B856
- Every structure of UniProt P63043
- Every structure of UniProt E1BQ43
- Elsewhere: RCSB PDB 4YJ2 · PDBe 4YJ2 · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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