Research workbench
The crystal structure of human eefsec in complex with gdpnp
Analyse The crystal structure of human eefsec in complex with gdpnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IZM
- Type
- protein
- Length
- 955 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Selenocysteine-specific elongation factor
- UniProt
- P57772
- Ligands
- GNP, MN
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Selenocysteine-specific elongation factor | protein | 460 | 16% helix, 30% strand | P57772 |
| B | Selenocysteine-specific elongation factor | protein | 495 | 16% helix, 35% strand | P57772 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.66 | 0.77 | 69 | empty |
| 2 | 407 | 0.64 | 0.78 | 60 | MN, GNP |
| 3 | 398 | 0.62 | 0.77 | 47 | empty |
| 4 | 362 | 0.61 | 0.78 | 41 | empty |
| 5 | 55 | 0.42 | 0.82 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 503 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 modified (engineered).
Compared structures
- 5IZM · The crystal structure of human eEFSec in complex with GDPNP · the same entry in another collection · chain A against A, TM-score 1.00
- P57772 · AlphaFold monomer V2.0 prediction for selenocysteine-specific elongation factor (P57772) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P57772
- Elsewhere: RCSB PDB 5IZM · PDBe 5IZM · UniProt P57772
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