Research workbench
Predicting the conformational variability of abl tyrosine kinase using molecular dynamics simulations and markov state models
Analyse Predicting the conformational variability of abl tyrosine kinase using… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BL8
- Type
- protein
- Length
- 538 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
- PVB, SO4
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 270 | 42% helix, 19% strand | P00519 |
| B | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 268 | 41% helix, 19% strand | P00519 |
Ligands and binding sites
- PVB · Purvalanol B · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.70 | 0.79 | 56 | PVB |
| 2 | 370 | 0.58 | 0.75 | 48 | PVB |
| 3 | 57 | 0.50 | 0.86 | 14 | empty |
| 4 | 66 | 0.50 | 0.84 | 15 | empty |
| 5 | 144 | 0.39 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 60 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6BL8 · Predicting the Conformational Variability of Abl Tyrosine Kinase Using Molecular Dynamics… · 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 B 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 6BL8 · PDBe 6BL8 · UniProt P00519
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