Research workbench
An engineered Axl 'decoy receptor' effectively silences the Gas6-Axl signaling axis
Analyse An engineered Axl 'decoy receptor' effectively silences the Gas6-Axl signaling… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RA0
- Type
- protein
- Length
- 1,145 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.07
- Source
- Homo sapiens
- Molecule
- Growth arrest-specific protein 6; Tyrosine-protein kinase receptor UFO
- EC
- 2.7.10.1
- UniProt
- P30530
- Ligands
- NAG, CA, NI, SO4, CL
- Pockets
- 16 · best druggability 0.60
Structure
x-ray diffraction · resolution 3.07 · 3 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Growth arrest-specific protein 6 | protein | 386 | 8% helix, 43% strand | — |
| B | Growth arrest-specific protein 6 | protein | 377 | 8% helix, 45% strand | — |
| C, D | Tyrosine-protein kinase receptor UFO (EC 2.7.10.1) | protein | 191 | 2% helix, 54% strand | P30530 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C, B, D
- CA · Calcium ion · metal · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains C, D
- SO4 · Sulfate ion · ion · 2 copies · chains C, D
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.60 | 0.83 | 30 | empty |
| 2 | 109 | 0.54 | 0.83 | 26 | empty |
| 3 | 146 | 0.54 | 0.81 | 30 | empty |
| 4 | 133 | 0.53 | 0.81 | 27 | empty |
| 5 | 173 | 0.51 | 0.78 | 30 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1197 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1195 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 513 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 501 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4RA0 · An engineered axl 'decoy receptor' effectively silences the GAS6-axl signaling axis · the same entry in another collection · chain A against A, TM-score 1.00
- P30530 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase receptor ufo (P30530) · a predicted model of the same protein · chain C 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 P30530
- Elsewhere: RCSB PDB 4RA0 · PDBe 4RA0 · UniProt P30530
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