Research workbench
Cryo EM density of microtubule assembled from human TUBB3-D417H mutant
Analyse Cryo EM density of microtubule assembled from human TUBB3-D417H mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IJ9
- Type
- protein
- Length
- 856 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1B chain; Tubulin beta-3 chain
- UniProt
- P68363, Q13509
- Ligands
- GTP, GDP, MG
- Pockets
- 9 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1B chain | protein | 430 | 47% helix, 17% strand | P68363 |
| B | Tubulin beta-3 chain | protein | 426 | 48% helix, 18% strand | Q13509 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.83 | 0.95 | 44 | GTP, MG |
| 2 | 245 | 0.61 | 0.81 | 46 | GDP |
| 3 | 311 | 0.60 | 0.78 | 37 | empty |
| 4 | 211 | 0.51 | 0.76 | 23 | empty |
| 5 | 149 | 0.45 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1879 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5IJ9 · Cryo EM density of microtubule assembled from human TUBB3-D417H mutant · the same entry in another collection · chain A against A, TM-score 1.00
- P68363 · AlphaFold monomer V2.0 prediction for tubulin alpha-1B chain (P68363) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q13509 · AlphaFold monomer V2.0 prediction for tubulin beta-3 chain (Q13509) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P68363
- Every structure of UniProt Q13509
- Elsewhere: RCSB PDB 5IJ9 · PDBe 5IJ9 · UniProt P68363 · UniProt Q13509
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