Research workbench
Yeast tubulin polymerized with GTP in vitro
Analyse Yeast tubulin polymerized with GTP in vitro in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W3F
- Type
- protein
- Length
- 867 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.7
- Source
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Molecule
- Tubulin alpha-1 chain; Tubulin beta chain
- UniProt
- P09733, P02557
- Ligands
- GTP, GDP, MG
- Pockets
- 11 · best druggability 0.82
Structure
electron microscopy · resolution 3.7 · 2 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1 chain | protein | 440 | 44% helix, 16% strand | P09733 |
| B | Tubulin beta chain | protein | 427 | 41% helix, 11% strand | P02557 |
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
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.82 | 0.87 | 81 | MG, GTP |
| 2 | 74 | 0.66 | 0.92 | 34 | empty |
| 3 | 322 | 0.64 | 0.80 | 38 | GDP |
| 4 | 255 | 0.58 | 0.79 | 41 | empty |
| 5 | 72 | 0.55 | 0.88 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1775 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5W3F · Yeast tubulin polymerized with GTP in vitro · the same entry in another collection · chain A against A, TM-score 1.00
- P09733 · AlphaFold monomer V2.0 prediction for tubulin alpha-1 chain (P09733) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P02557 · AlphaFold monomer V2.0 prediction for tubulin beta chain (P02557) · a predicted model of the same protein · chain B 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 P09733
- Every structure of UniProt P02557
- Elsewhere: RCSB PDB 5W3F · PDBe 5W3F · UniProt P09733 · UniProt P02557
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