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Crystal structure of unphosphorylated human pkr kinase domain in complex with ADP
Analyse Crystal structure of unphosphorylated human pkr kinase domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D3K
- Type
- protein
- Length
- 770 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interferon-induced, double-stranded RNA-activated protein kinase
- EC
- 2.7.11.1, 2.7.10.2
- UniProt
- P19525
- Ligands
- ADP, MG, SO4, PO4
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Interferon-induced, double-stranded RNA-activated protein kinase (EC 2.7.11.1, 2.7.10.2) | protein | 254 | 41% helix, 21% strand | P19525 |
| A | Interferon-induced, double-stranded RNA-activated protein kinase (EC 2.7.11.1, 2.7.10.2) | protein | 258 | 41% helix, 20% strand | P19525 |
| C | Interferon-induced, double-stranded RNA-activated protein kinase (EC 2.7.11.1, 2.7.10.2) | protein | 258 | 41% helix, 19% strand | P19525 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains B, A, C
- MG · Magnesium ion · metal · 3 copies · chains B, A, C
- SO4 · Sulfate ion · ion · 7 copies · chains B, A, C
- PO4 · Phosphate ion · ion · 4 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.75 | 0.99 | 21 | empty |
| 2 | 352 | 0.68 | 0.82 | 50 | empty |
| 3 | 379 | 0.64 | 0.79 | 44 | ADP, MG |
| 4 | 289 | 0.64 | 0.80 | 32 | ADP, PO4, MG |
| 5 | 251 | 0.60 | 0.79 | 32 | ADP, MG |
Interfaces
2 interfaces between chains.
- B–A · 1343 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 899 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6D3K · Crystal structure of unphosphorylated human PKR kinase domain in complex with ADP · the same entry in another collection · chain B against B, 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 C against A, TM-score 0.98
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 P19525
- Elsewhere: RCSB PDB 6D3K · PDBe 6D3K · UniProt P19525
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