Research workbench
Crystal structure of bacterial selenocysteine-specific elongation factor EF-Sec
Analyse Crystal structure of bacterial selenocysteine-specific elongation factor EF-Sec in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZU9
- Type
- protein
- Length
- 582 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.191
- Source
- Aquifex aeolicus VF5
- Molecule
- Elongation factor SelB
- UniProt
- O67141
- Ligands
- GNP, CYS, MG, SO4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · resolution 3.191 · 1 distinct chain · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor SelB | protein | 582 | 35% helix, 28% strand | O67141 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- CYS · Cysteine · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.69 | 0.80 | 64 | empty |
| 2 | 105 | 0.47 | 0.80 | 26 | GNP, MG |
| 3 | 125 | 0.40 | 0.75 | 26 | CYS |
| 4 | 57 | 0.32 | 0.76 | 14 | empty |
| 5 | 51 | 0.30 | 0.76 | 15 | empty |
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 4ZU9 · Crystal structure of bacterial selenocysteine-specific elongation factor ef-sec · the same entry in another collection · chain A against A, 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 O67141
- Elsewhere: RCSB PDB 4ZU9 · PDBe 4ZU9 · UniProt O67141
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