Research workbench
Crystal structure of the chimerical mutant CAPABK55M protein
Analyse Crystal structure of the chimerical mutant CAPABK55M protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VED
- Type
- protein
- Length
- 506 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane protein CAPA1, protein tyrosine kinase
- UniProt
- A8YPQ6, A8YPQ5
- Ligands
- ADP, MG
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Membrane protein CAPA1, protein tyrosine kinase | protein | 252 | 37% helix, 18% strand | A8YPQ6, A8YPQ5 |
| B | Membrane protein CAPA1, protein tyrosine kinase | protein | 254 | 37% helix, 17% strand | A8YPQ6, A8YPQ5 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.56 | 0.77 | 31 | empty |
| 2 | 120 | 0.44 | 0.77 | 27 | empty |
| 3 | 77 | 0.38 | 0.78 | 25 | ADP, MG |
| 4 | 69 | 0.30 | 0.74 | 18 | MG |
Interfaces
1 interface between chains.
- A–B · 1062 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2VED · crystal structure of the chimerical mutant CapABK55M protein · the same entry in another collection · chain A against A, TM-score 1.00
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 A8YPQ6
- Every structure of UniProt A8YPQ5
- Elsewhere: RCSB PDB 2VED · PDBe 2VED · UniProt A8YPQ6 · UniProt A8YPQ5
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