Research workbench
Cryo-EM MAP of protofilament of microtubule doublet
Analyse Cryo-EM MAP of protofilament of microtubule doublet in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UCY
- Type
- protein
- Length
- 870 residues
- Chains
- 2
- 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
- 16 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 441 | 45% helix, 15% strand | P41351 |
| B | Tubulin beta chain | protein | 429 | 47% helix, 14% strand | P41352 |
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, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.82 | 0.97 | 43 | empty |
| 2 | 198 | 0.78 | 0.93 | 45 | empty |
| 3 | 101 | 0.78 | 0.97 | 29 | empty |
| 4 | 74 | 0.75 | 0.98 | 24 | empty |
| 5 | 68 | 0.70 | 0.95 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1870 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 covalent (covalent ligand).
Compared structures
- 5UCY · Cryo-EM map of protofilament of 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 B 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 A 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 5UCY · PDBe 5UCY · UniProt P41351 · UniProt P41352
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