Research workbench
Pkr kinase domain- EIF2ALPHA- AMP-pnp complex.
Analyse Pkr kinase domain- EIF2ALPHA- AMP-pnp complex. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A19
- Type
- protein
- Length
- 632 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 2 alpha subunit; Interferon-induced…
- EC
- 2.7.1.-
- UniProt
- P20459, P19525
- Ligands
- ANP, MG, PO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 2 alpha subunit | protein | 165 | 41% helix, 22% strand | P20459 |
| B | Interferon-induced, double-stranded RNA-activated protein kinase (EC 2.7.1.-) | protein | 264 | 41% helix, 21% strand | P19525 |
| C | Interferon-induced, double-stranded RNA-activated protein kinase (EC 2.7.1.-) | protein | 203 | 34% helix, 26% strand | P19525 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains B, C
- MG · Magnesium ion · metal · 4 copies · chains B, C
- PO4 · Phosphate ion · ion · chains C
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 | 70 | 0.72 | 0.97 | 20 | empty |
| 2 | 405 | 0.69 | 0.81 | 50 | empty |
| 3 | 583 | 0.67 | 0.77 | 49 | MG, ANP |
| 4 | 290 | 0.58 | 0.77 | 37 | MG, ANP |
| 5 | 147 | 0.50 | 0.79 | 31 | empty |
Interfaces
2 interfaces between chains.
- B–C · 937 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 672 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 2A19 · PKR kinase domain- eIF2alpha- AMP-PNP complex. · the same entry in another collection · chain A against A, TM-score 1.00
- P19525 · AlphaFold monomer V2.0 prediction for interferon-induced, double- stranded RNA-activated… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P20459 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 2 subunit… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P20459
- Every structure of UniProt P19525
- Elsewhere: RCSB PDB 2A19 · PDBe 2A19 · UniProt P20459 · UniProt P19525
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