MolNFT v1 · #122774 · protein
The crystal structure of human eefsec in complex with GDP
5IZK · Selenocysteine-specific elongation factor: “The crystal structure of human eefsec in complex with GDP”. X-ray diffraction, 1 ligand (GDP), 19 pockets (best druggability 0.76). MolNFT v1 #122774 on GenesisL1: 3D structure, binding…
- PDB
- 5IZK
- Type
- protein
- Length
- 931 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Selenocysteine-specific elongation factor
- UniProt
- P57772
- Ligands
- GDP
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Selenocysteine-specific elongation factor | protein | 480 | 14% helix, 30% strand | P57772 |
| B | Selenocysteine-specific elongation factor | protein | 451 | 16% helix, 29% strand | P57772 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1144 | 0.76 | 0.79 | 122 | empty |
| 2 | 590 | 0.76 | 0.82 | 67 | empty |
| 3 | 384 | 0.75 | 0.85 | 56 | empty |
| 4 | 174 | 0.72 | 0.90 | 31 | empty |
| 5 | 377 | 0.71 | 0.83 | 48 | empty |
Interfaces
1 interface between chains.
- A–B · 622 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5IZK · The crystal structure of human eEFSec in complex with GDP · 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 0.91
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 5IZK · PDBe 5IZK · UniProt P57772
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