MolNFT v1 · #126506 · protein
Mechanism of microtubule minus-end recognition and protection by camsap proteins
5M50 · Tubulin alpha chain: “Mechanism of microtubule minus-end recognition and protection by camsap proteins”. Electron microscopy, 4 ligands (GTP, GDP, TA1), 20 pockets (best druggability 0.84). MolNFT v1 #126506 on GenesisL1: 3D…
- PDB
- 5M50
- Type
- protein
- Length
- 1,826 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta-2B chain; Calmodulin-regulated spectrin-associated…
- UniProt
- F2Z4C1, Q6B856, Q80VC9
- Ligands
- GTP, GDP, TA1, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A | Tubulin alpha chain | protein | 428 | 43% helix, 16% strand | F2Z4C1 |
| E, B | Tubulin beta-2B chain | protein | 426 | 49% helix, 18% strand | Q6B856 |
| C | Calmodulin-regulated spectrin-associated protein 3 | protein | 118 | 21% helix, 32% strand | Q80VC9 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains D, E, A, B
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains E, B
- TA1 · Taxol · ligand · 2 copies · chains E, B
- MG · Magnesium ion · metal · 2 copies · chains D, E, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.84 | 0.96 | 45 | GTP, MG |
| 2 | 271 | 0.84 | 0.95 | 44 | GTP, MG |
| 3 | 861 | 0.78 | 0.81 | 68 | empty |
| 4 | 1083 | 0.77 | 0.79 | 77 | empty |
| 5 | 779 | 0.77 | 0.81 | 80 | empty |
Interfaces
8 interfaces between chains.
- D–E · 1915 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1905 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 553 Ų buried · 4 hydrogen bonds · protein-protein
- E–B · 466 Ų buried · 5 hydrogen bonds · protein-protein
- D–A · 399 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5M50 · Mechanism of microtubule minus-end recognition and protection by CAMSAP proteins · the same entry in another collection · chain D against D, TM-score 1.00
- Q80VC9 · AlphaFold monomer V2.0 prediction for calmodulin-regulated spectrin- associated protein 3… · a predicted model of the same protein · chain C against A, TM-score 0.94
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 F2Z4C1
- Every structure of UniProt Q6B856
- Every structure of UniProt Q80VC9
- Elsewhere: RCSB PDB 5M50 · PDBe 5M50 · UniProt F2Z4C1 · UniProt Q6B856 · UniProt Q80VC9
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