Research workbench
DYRK1A in complex with nitro benzothiazole fragment
Analyse DYRK1A in complex with nitro benzothiazole fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A54
- Type
- protein
- Length
- 1,350 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual specificity tyrosine-phosphorylation-regulated kinase 1A
- EC
- 2.7.12.1
- UniProt
- Q13627
- Ligands
- 5PW
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 342 | 35% helix, 18% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 340 | 36% helix, 17% strand | Q13627 |
| C | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 333 | 37% helix, 15% strand | Q13627 |
| D | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 335 | 35% helix, 19% strand | Q13627 |
Ligands and binding sites
- 5PW · N-(6-nitro-1,3-benzothiazol-2-yl)ethanamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.85 | 0.87 | 100 | empty |
| 2 | 1051 | 0.82 | 0.83 | 85 | empty |
| 3 | 890 | 0.78 | 0.81 | 79 | 5PW |
| 4 | 1066 | 0.78 | 0.79 | 89 | 5PW |
| 5 | 707 | 0.78 | 0.82 | 86 | 5PW |
Interfaces
6 interfaces between chains.
- C–D · 1273 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1243 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 958 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 749 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 25 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 1 disulfide (phosphorylation, disulfide).
Compared structures
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 5A54 · PDBe 5A54 · UniProt Q13627
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