Research workbench
Crystal structure of 5-bromoindoline-2,3-dione covalently bound to the pH domain of BRUTON'S tyrosine kinase
Analyse Crystal structure of 5-bromoindoline-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
- 6TVN
- Type
- protein
- Length
- 615 residues
- Chains
- 4
- 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
- NYQ, ZN, MG
- Pockets
- 9 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 160 | 17% helix, 38% strand | Q06187 |
| B | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 150 | 15% helix, 41% strand | Q06187 |
| C | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 157 | 16% helix, 38% strand | Q06187 |
| D | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 148 | 16% helix, 39% strand | Q06187 |
Ligands and binding sites
- NYQ · 5-bromanyl-1,3-dihydroindol-2-one · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.59 | 0.76 | 44 | empty |
| 2 | 184 | 0.54 | 0.79 | 28 | NYQ |
| 3 | 132 | 0.49 | 0.79 | 24 | empty |
| 4 | 128 | 0.45 | 0.77 | 31 | empty |
| 5 | 60 | 0.45 | 0.83 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1098 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 272 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 146 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 92 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 41 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6TVN · Crystal Structure of 5-bromoindoline-2,3-dione covalently bound to the PH domain of… · the same entry in another collection · chain D against D, TM-score 1.00
- Q06187 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase btk (Q06187) · a predicted model of the same protein · chain D 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 6TVN · PDBe 6TVN · UniProt Q06187
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