MolNFT v1 · #126590 · protein
Tubulin-MTD147 complex
5M7G · Tubulin alpha-1B chain: “Tubulin-MTD147 complex”. X-ray diffraction, 6 ligands (GTP, FB7, GDP), 20 pockets (best druggability 0.88). MolNFT v1 #126590 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5M7G
- Type
- protein
- Length
- 2,165 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, FB7, 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 | 436 | 46% helix, 18% strand | P81947 |
| B | Tubulin beta-2B chain | protein | 422 | 49% helix, 19% strand | Q6B856 |
| C | Tubulin alpha-1B chain | protein | 440 | 47% helix, 17% strand | P81947 |
| D | Tubulin beta-2B chain | protein | 418 | 51% helix, 20% strand | Q6B856 |
| E | Stathmin-4 | protein | 123 | 77% helix, 14% strand | P63043 |
| F | Tubulin-tyrosine ligase | protein | 326 | 30% helix, 23% strand | E1BQ43 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D
- FB7 · 5-(2,6-dimorpholin-4-ylpyridin-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
- GOL · Glycerol · additive · 2 copies · chains A, F
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1191 | 0.88 | 0.89 | 130 | GTP, MG, FB7 |
| 2 | 1152 | 0.82 | 0.83 | 128 | GDP, MG |
| 3 | 1160 | 0.80 | 0.82 | 108 | GTP, MG, FB7 |
| 4 | 1144 | 0.76 | 0.79 | 108 | MG, ACP |
| 5 | 81 | 0.71 | 0.96 | 23 | empty |
Interfaces
9 interfaces between chains.
- A–E · 1638 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1386 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1322 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 937 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 806 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5M7G · Tubulin-MTD147 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 5M7G · PDBe 5M7G · UniProt P81947 · UniProt Q6B856 · UniProt P63043 · UniProt E1BQ43
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