MolNFT v1 · #52315 · protein
Crystal structure of the human dual specificity tyrosine- phosphorylation-regulated kinase 1A
2VX3 · Dual specificity tyrosine-phosphorylation- regulated kinase…: “Crystal structure of the human dual specificity tyrosine- phosphorylation-regulated kinase 1A”. X-ray diffraction, 3 ligands (D15, CL, SO4), 16 pockets (best…
- PDB
- 2VX3
- Type
- protein
- Length
- 1,370 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
- D15, CL, SO4
- Pockets
- 16 · best druggability 0.82
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 | 347 | 37% helix, 18% strand | Q13627 |
| B | Dual specificity tyrosine-phosphorylation- regulated kinase 1A (EC 2.7.12.1) | protein | 341 | 37% helix, 18% strand | Q13627 |
| C | Dual specificity tyrosine-phosphorylation- regulated kinase 1A (EC 2.7.12.1) | protein | 339 | 37% helix, 18% strand | Q13627 |
| D | Dual specificity tyrosine-phosphorylation- regulated kinase 1A (EC 2.7.12.1) | protein | 343 | 37% helix, 18% strand | Q13627 |
Ligands and binding sites
- D15 · N-(5-{[(2S)-4-amino-2-(3-chlorophenyl)butanoyl]amino}-1H-indazol-3-yl)benzamide · ligand · 4 copies · chains A, B, D, C
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, D, C
- P6G · Hexaethylene glycol · additive · 8 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.82 | 0.83 | 70 | CL |
| 2 | 765 | 0.75 | 0.80 | 74 | D15, CL, SO4, P6G |
| 3 | 390 | 0.67 | 0.80 | 40 | D15, CL, SO4 |
| 4 | 322 | 0.66 | 0.81 | 32 | D15, CL, SO4 |
| 5 | 383 | 0.65 | 0.79 | 40 | D15, CL, SO4 |
Interfaces
3 interfaces between chains.
- B–D · 613 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 572 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 287 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 2VX3 · Crystal structure of the human dual specificity tyrosine- phosphorylation-regulated… · the same entry in another collection · chain D against D, TM-score 1.00
- Q13627 · AlphaFold monomer V2.0 prediction for dual specificity tyrosine… · 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 Q13627
- Elsewhere: RCSB PDB 2VX3 · PDBe 2VX3 · UniProt Q13627
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