MolNFT v1 · #30547 · protein
High-resolution crystallographic analysis of the autoinhibited conformation of a human death-associated protein kinase
2A2A · Death-associated protein kinase 2: “High-resolution crystallographic analysis of the autoinhibited conformation of a human death-associated…”. X-ray diffraction, 2 ligands (NA, CL), 12 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 2A2A
- Type
- protein
- Length
- 1,213 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Death-associated protein kinase 2
- EC
- 2.7.1.37
- UniProt
- Q9UIK4
- Ligands
- NA, CL
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Death-associated protein kinase 2 (EC 2.7.1.37) | protein | 304 | 38% helix, 18% strand | Q9UIK4 |
| B, C, D | Death-associated protein kinase 2 (EC 2.7.1.37) | protein | 303 | 39% helix, 18% strand | Q9UIK4 |
Ligands and binding sites
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, C, D
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.81 | 0.83 | 90 | GOL |
| 2 | 711 | 0.80 | 0.84 | 77 | NA |
| 3 | 593 | 0.80 | 0.86 | 80 | CL, DTT, GOL |
| 4 | 608 | 0.80 | 0.85 | 73 | NA, GOL |
| 5 | 309 | 0.63 | 0.80 | 29 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1567 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1469 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 807 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2A2A · High-resolution crystallographic analysis of the autoinhibited conformation of a human… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9UIK4 · AlphaFold monomer V2.0 prediction for death-associated protein kinase 2 (Q9UIK4) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q9UIK4
- Elsewhere: RCSB PDB 2A2A · PDBe 2A2A · UniProt Q9UIK4
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