MolNFT v1 · #53225 · protein
Human dual-specificity tyrosine-phosphorylation-regulated kinase 1A in complex with a consensus substrate peptide
2WO6 · Dual specificity tyrosine-phosphorylation- regulated kinase…: “Human dual-specificity tyrosine-phosphorylation-regulated kinase 1A in complex with a consensus substrate…”. X-ray diffraction, 2 ligands (D15, CL), 7 pockets (best…
- PDB
- 2WO6
- Type
- protein
- Length
- 693 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual specificity tyrosine-phosphorylation- regulated kinase 1A; Artificial consensus…
- EC
- 2.7.12.1
- UniProt
- Q13627
- Ligands
- D15, CL
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity tyrosine-phosphorylation- regulated kinase 1A (EC 2.7.12.1) | protein | 345 | 38% helix, 18% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation- regulated kinase 1A (EC 2.7.12.1) | protein | 340 | 36% helix, 18% strand | Q13627 |
| C | Artificial consensus sequence | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- D15 · N-(5-{[(2S)-4-amino-2-(3-chlorophenyl)butanoyl]amino}-1H-indazol-3-yl)benzamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains 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 | 385 | 0.69 | 0.81 | 40 | D15, CL |
| 2 | 359 | 0.66 | 0.80 | 41 | D15 |
| 3 | 346 | 0.62 | 0.78 | 33 | empty |
| 4 | 175 | 0.54 | 0.80 | 29 | empty |
| 5 | 67 | 0.41 | 0.80 | 16 | empty |
Interfaces
2 interfaces between chains.
- B–C · 576 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 499 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2WO6 · Human Dual-Specificity Tyrosine-Phosphorylation-Regulated Kinase 1A in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13627 · AlphaFold monomer V2.0 prediction for dual specificity tyrosine… · a predicted model of the same protein · chain B 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 Q13627
- Elsewhere: RCSB PDB 2WO6 · PDBe 2WO6 · UniProt Q13627
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