MolNFT v1 · #122775 · protein
The crystal structure of human eefsec in complex with gdpcp
5IZL · Selenocysteine-specific elongation factor: “The crystal structure of human eefsec in complex with gdpcp”. X-ray diffraction, 2 ligands (GCP, MG), 13 pockets (best druggability 0.71). MolNFT v1 #122775 on GenesisL1: 3D structure…
- PDB
- 5IZL
- Type
- protein
- Length
- 1,012 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Selenocysteine-specific elongation factor
- UniProt
- P57772
- Ligands
- GCP, MG
- Pockets
- 13 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Selenocysteine-specific elongation factor | protein | 514 | 18% helix, 38% strand | P57772 |
| B | Selenocysteine-specific elongation factor | protein | 498 | 19% helix, 36% strand | P57772 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 645 | 0.71 | 0.78 | 81 | empty |
| 2 | 309 | 0.65 | 0.81 | 41 | empty |
| 3 | 307 | 0.57 | 0.77 | 38 | empty |
| 4 | 278 | 0.56 | 0.77 | 33 | empty |
| 5 | 223 | 0.53 | 0.77 | 38 | MG, GCP |
Interfaces
1 interface between chains.
- A–B · 607 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5IZL · The crystal structure of human eEFSec in complex with GDPCP · 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 B against A, TM-score 0.94
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 5IZL · PDBe 5IZL · UniProt P57772
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