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Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament arrangement, bound to 53% GTP/47% and 2 Na+
Analyse Odinarchaeota tubulin (OdinTubulin) H393D mutant, in a protofilament… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EVD
- Type
- protein
- Length
- 422 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.45
- Source
- Odinarchaeota archaeon (strain LCB_4)
- Molecule
- Tubulin-like protein
- UniProt
- A0A1Q9N9N5
- Ligands
- GTP, GDP, NA
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · resolution 1.45 · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Tubulin-like protein | protein | 422 | 45% helix, 19% strand | A0A1Q9N9N5 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- NA · Sodium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.56 | 0.80 | 34 | GTP, GDP, NA |
| 2 | 112 | 0.45 | 0.78 | 20 | empty |
| 3 | 67 | 0.45 | 0.82 | 15 | empty |
| 4 | 61 | 0.33 | 0.76 | 15 | empty |
| 5 | 62 | 0.29 | 0.74 | 16 | empty |
Compared structures
- 7EVD · Odinarchaeota tubulin (odintubulin) H393D mutant, in a protofilament arrangement, bound… · the same entry in another collection · chain B against B, TM-score 1.00
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 A0A1Q9N9N5
- Elsewhere: RCSB PDB 7EVD · PDBe 7EVD · UniProt A0A1Q9N9N5
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