MolNFT v1 · #82414 · protein
Archaeal protein
3VMF · Elongation factor 1-alpha: “Archaeal protein”. X-ray diffraction, 3 ligands (GTP, MG, SO4), 7 pockets (best druggability 0.81). MolNFT v1 #82414 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VMF
- Type
- protein
- Length
- 778 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor 1-alpha; Peptide chain release factor subunit 1
- UniProt
- Q9YAV0, Q9YAF1
- Ligands
- GTP, MG, SO4
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Elongation factor 1-alpha | protein | 427 | 23% helix, 35% strand | Q9YAV0 |
| B | Peptide chain release factor subunit 1 | protein | 351 | 42% helix, 23% strand | Q9YAF1 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.81 | 0.83 | 88 | empty |
| 2 | 224 | 0.66 | 0.84 | 31 | empty |
| 3 | 164 | 0.59 | 0.83 | 26 | GTP, MG |
| 4 | 336 | 0.57 | 0.75 | 29 | empty |
| 5 | 104 | 0.50 | 0.81 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1633 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3VMF · Archaeal protein · the same entry in another collection · chain A against A, TM-score 1.00
- Q9YAV0 · AlphaFold monomer V2.0 prediction for elongation factor 1-alpha (Q9YAV0) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9YAF1 · AlphaFold monomer V2.0 prediction for peptide chain release factor subunit 1 (Q9YAF1) · a predicted model of the same protein · chain B against A, TM-score 0.75
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 Q9YAV0
- Every structure of UniProt Q9YAF1
- Elsewhere: RCSB PDB 3VMF · PDBe 3VMF · UniProt Q9YAV0 · UniProt Q9YAF1
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