Research workbench
The crystal structure of human ABL1 kinase domain in complex with ABL2-A5
Analyse The crystal structure of human ABL1 kinase domain in complex with ABL2-A5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W7Y
- Type
- protein
- Length
- 536 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase ABL1
- EC
- 2.7.10.2
- UniProt
- P00519
- Ligands
- 8IW
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 269 | 41% helix, 17% strand | P00519 |
| B | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 267 | 43% helix, 18% strand | P00519 |
Ligands and binding sites
- 8IW · 5-[3-(5-methanoyl-2-methoxy-4-oxidanyl-phenyl)-1~{H}-pyrrolo[2,3-b]pyridin-5-yl]-~{N},~{N}-dimethyl-pyridine-3-carboxamide · ligand · 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 | 748 | 0.76 | 0.81 | 76 | 8IW |
| 2 | 438 | 0.68 | 0.79 | 55 | 8IW |
| 3 | 79 | 0.49 | 0.83 | 19 | empty |
| 4 | 212 | 0.47 | 0.74 | 34 | empty |
| 5 | 70 | 0.46 | 0.82 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 748 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, phosphorylation).
Compared structures
- 7W7Y · The crystal structure of human abl1 kinase domain in complex with ABL2-A5 · the same entry in another collection · chain A against A, TM-score 1.00
- P00519 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase ABL1 (P00519) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P00519
- Elsewhere: RCSB PDB 7W7Y · PDBe 7W7Y · UniProt P00519
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