Research workbench
Crystal structure of 1,5-dimethylindoline-2,3-dione covalently bound to the pH domain of BRUTON'S tyrosine kinase mutant R28C
Analyse Crystal structure of 1,5-dimethylindoline-2,3-dione covalently bound to the pH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YYK
- Type
- protein
- Length
- 317 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase btk
- EC
- 2.7.10.2
- UniProt
- Q06187
- Ligands
- IS7, ZN, MG
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 164 | 15% helix, 35% strand | Q06187 |
| B | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 153 | 16% helix, 41% strand | Q06187 |
Ligands and binding sites
- IS7 · 1,5-dimethyl-3~{H}-indol-2-one · ligand · chains B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 471 | 0.62 | 0.76 | 41 | empty |
| 2 | 322 | 0.59 | 0.77 | 31 | empty |
| 3 | 69 | 0.43 | 0.81 | 19 | empty |
| 4 | 72 | 0.42 | 0.80 | 20 | empty |
| 5 | 55 | 0.28 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 472 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6YYK · Crystal Structure of 1,5-dimethylindoline-2,3-dione covalently bound to the PH domain of… · the same entry in another collection · chain A against A, TM-score 1.00
- Q06187 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase btk (Q06187) · a predicted model of the same protein · chain B 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 Q06187
- Elsewhere: RCSB PDB 6YYK · PDBe 6YYK · UniProt Q06187
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