Research workbench
Mutant L38M structure of PH0725 from Pyrococcus horikoshii OT3
Analyse Mutant L38M structure of PH0725 from Pyrococcus horikoshii OT3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EJK
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Pyrococcus horikoshii
- Molecule
- diphthine synthase
- EC
- 2.1.1.98
- UniProt
- O58456
- Ligands
- SAH, SO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.4 · 1 distinct chain · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | diphthine synthase (EC 2.1.1.98) | protein | 265 | 38% helix, 23% strand | O58456 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.75 | 0.84 | 59 | SO4, SAH |
| 2 | 445 | 0.74 | 0.83 | 47 | empty |
| 3 | 150 | 0.43 | 0.75 | 19 | empty |
| 4 | 104 | 0.41 | 0.77 | 16 | empty |
| 5 | 90 | 0.37 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2561 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
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 O58456
- Elsewhere: RCSB PDB 2EJK · PDBe 2EJK · UniProt O58456
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