MolNFT v1 · #100956 · protein
Human DYRK1A in complex with PKC412
4NCT · Dual specificity tyrosine-phosphorylation-regulated kinase…: “Human DYRK1A in complex with PKC412”. X-ray diffraction, 1 ligand (2K2), 8 pockets (best druggability 0.85). MolNFT v1 #100956 on GenesisL1: 3D structure, binding sites…
- PDB
- 4NCT
- Type
- protein
- Length
- 1,349 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
- 2K2
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 4 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 | 342 | 37% helix, 18% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 334 | 37% helix, 18% strand | Q13627 |
| C | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 341 | 36% helix, 18% strand | Q13627 |
| D | Dual specificity tyrosine-phosphorylation-regulated kinase 1A (EC 2.7.12.1) | protein | 332 | 37% helix, 19% strand | Q13627 |
Ligands and binding sites
- 2K2 · Pkc412 · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.85 | 0.86 | 109 | empty |
| 2 | 1120 | 0.85 | 0.85 | 124 | empty |
| 3 | 863 | 0.78 | 0.81 | 87 | 2K2 |
| 4 | 811 | 0.78 | 0.81 | 96 | 2K2 |
| 5 | 677 | 0.75 | 0.81 | 73 | 2K2 |
Interfaces
6 interfaces between chains.
- A–B · 1312 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1278 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1011 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1011 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 45 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 modified, 4 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 4NCT · PDBe 4NCT · UniProt Q13627
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