Research workbench
Cryo-EM structure of ciliary microtubule doublet
Analyse Cryo-EM structure of ciliary microtubule doublet in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UBQ
- Type
- protein
- Length
- 2,610 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain
- UniProt
- P41351, P41352
- Ligands
- GTP, GDP, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E, A | Tubulin alpha chain | protein | 441 | 45% helix, 15% strand | P41351 |
| D, F, B | Tubulin beta chain | protein | 429 | 47% helix, 14% strand | P41352 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains C, D, E, F, A, B
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains D, E, F, C, B
- MG · Magnesium ion · metal · 3 copies · chains C, D, E, F, 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 | 593 | 0.83 | 0.88 | 92 | empty |
| 2 | 569 | 0.82 | 0.88 | 91 | empty |
| 3 | 187 | 0.82 | 0.97 | 42 | empty |
| 4 | 186 | 0.82 | 0.96 | 43 | empty |
| 5 | 190 | 0.82 | 0.96 | 45 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1867 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1867 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1865 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1704 Ų buried · 46 hydrogen bonds · protein-protein
- C–B · 1697 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 covalent (covalent ligand).
Compared structures
- 5UBQ · Cryo-EM structure of ciliary microtubule doublet · the same entry in another collection · chain B against B, TM-score 1.00
- P41352 · AlphaFold monomer V2.0 prediction for tubulin beta chain (P41352) · a predicted model of the same protein · chain D against A, TM-score 0.98
- P41351 · AlphaFold monomer V2.0 prediction for tubulin alpha chain (P41351) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 P41351
- Every structure of UniProt P41352
- Elsewhere: RCSB PDB 5UBQ · PDBe 5UBQ · UniProt P41351 · UniProt P41352
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