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Crystal structure of catalytic domain of the proto-oncogene tyrosine- protein kinase mer in complex with ADP
Analyse Crystal structure of catalytic domain of the proto-oncogene tyrosine- protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BRB
- Type
- protein
- Length
- 531 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase mer
- EC
- 2.7.10.1
- UniProt
- Q12866
- Ligands
- ADP, MG, CL
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 260 | 41% helix, 17% strand | Q12866 |
| B | Proto-oncogene tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 271 | 40% helix, 18% strand | Q12866 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.69 | 0.77 | 73 | ADP, CL, MG |
| 2 | 323 | 0.62 | 0.79 | 31 | empty |
| 3 | 328 | 0.62 | 0.78 | 33 | ADP, MG |
Interfaces
1 interface between chains.
- A–B · 1063 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3BRB · Crystal structure of catalytic domain of the proto-oncogene tyrosine-protein kinase MER… · the same entry in another collection · chain A against A, TM-score 1.00
- Q12866 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase mer (Q12866) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q12866
- Elsewhere: RCSB PDB 3BRB · PDBe 3BRB · UniProt Q12866
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