MolNFT v1 · #126625 · protein
Tubulin-MTD265 complex
5M8G · Tubulin alpha-1B chain: “Tubulin-MTD265 complex”. X-ray diffraction, 6 ligands (GTP, 918, GDP), 20 pockets (best druggability 0.88). MolNFT v1 #126625 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5M8G
- Type
- protein
- Length
- 2,184 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, 918, GDP, ACP, MG, CA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 440 | 46% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 423 | 49% helix, 20% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 440 | 47% helix, 17% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 427 | 49% helix, 19% strand | Q6B856 |
| E | Stathmin-4 | protein | 123 | 77% helix, 13% strand | P63043 |
| F | Tubulin-tyrosine ligase | protein | 331 | 34% helix, 23% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- 918 · 5-(2-morpholin-4-yl-6-pyrrolidin-1-yl-pyrimidin-4-yl)-4-(trifluoromethyl)pyridin-2-amine · ligand · 2 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, D
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains F
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, F
- CA · Calcium ion · metal · 5 copies · chains A, E, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.88 | 0.90 | 134 | GTP, MG, 918 |
| 2 | 921 | 0.84 | 0.86 | 122 | GDP, MG |
| 3 | 882 | 0.84 | 0.86 | 90 | GTP, MG, 918 |
| 4 | 1152 | 0.75 | 0.78 | 91 | MG |
| 5 | 335 | 0.71 | 0.84 | 32 | MES |
Interfaces
9 interfaces between chains.
- A–E · 1614 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1510 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1358 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 945 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 935 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5M8G · Tubulin-MTD265 complex · 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 5M8G · PDBe 5M8G · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.