Research workbench
High-affinity axl decoy receptor
Analyse High-affinity axl decoy receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VXZ
- Type
- protein
- Length
- 956 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Growth arrest-specific protein 6; Tyrosine-protein kinase receptor ufo
- EC
- 2.7.10.1
- UniProt
- Q14393, P30530
- Ligands
- NAG, CA, CL
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Growth arrest-specific protein 6 | protein | 376 | 10% helix, 46% strand | Q14393 |
| C, D | Tyrosine-protein kinase receptor ufo (EC 2.7.10.1) | protein | 102 | 3% helix, 55% 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
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 319 | 0.70 | 0.84 | 54 | empty |
| 2 | 298 | 0.65 | 0.81 | 44 | empty |
| 3 | 134 | 0.53 | 0.81 | 29 | empty |
| 4 | 116 | 0.50 | 0.80 | 27 | empty |
| 5 | 89 | 0.44 | 0.80 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1251 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1159 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 334 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5VXZ · High-affinity AXL decoy receptor · the same entry in another collection · chain A against A, TM-score 1.00
- Q14393 · AlphaFold monomer V2.0 prediction for growth arrest-specific protein 6 (Q14393) · a predicted model of the same protein · chain A against A, TM-score 0.98
- 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 0.94
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 Q14393
- Every structure of UniProt P30530
- Elsewhere: RCSB PDB 5VXZ · PDBe 5VXZ · UniProt Q14393 · UniProt P30530
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