Research workbench
Structure of a minimal GAS6-axl complex
Analyse Structure of a minimal GAS6-axl complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C5D
- Type
- protein
- Length
- 1,142 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Growth-arrest-specific protein 6 precursor; Tyrosine-protein kinase receptor ufo
- EC
- 2.7.1.112
- UniProt
- Q14393, P30530
- Ligands
- NAG, CA, NI, SO4
- Pockets
- 13 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Growth-arrest-specific protein 6 precursor | protein | 380 | 7% helix, 42% strand | Q14393 |
| C, D | Tyrosine-protein kinase receptor ufo (EC 2.7.1.112) | protein | 191 | 0% 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 · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.66 | 0.90 | 27 | empty |
| 2 | 94 | 0.63 | 0.89 | 24 | empty |
| 3 | 133 | 0.60 | 0.84 | 27 | empty |
| 4 | 155 | 0.48 | 0.77 | 27 | empty |
| 5 | 148 | 0.45 | 0.76 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1189 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1176 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 447 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 443 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2C5D · Structure of a minimal Gas6-Axl complex · 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 B against A, TM-score 0.99
- 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 2C5D · PDBe 2C5D · UniProt Q14393 · UniProt P30530
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