Research workbench
Crystal structure of jaml in complex with the stimulatory antibody HL4E10
Analyse Crystal structure of jaml in complex with the stimulatory antibody HL4E10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MJ9
- Type
- protein
- Length
- 648 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Junctional adhesion molecule-like; Stimulatory hamster antibody HL4E10 Fab light chain…
- UniProt
- Q80UL9
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Junctional adhesion molecule-like | protein | 229 | 8% helix, 47% strand | Q80UL9 |
| L | Stimulatory hamster antibody HL4E10 Fab light chain | protein | 209 | 7% helix, 51% strand | — |
| H | Stimulatory hamster antibody HL4E10 Fab heavy chain | protein | 210 | 3% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.60 | 0.79 | 45 | empty |
| 2 | 439 | 0.56 | 0.74 | 57 | empty |
| 3 | 149 | 0.45 | 0.76 | 27 | empty |
| 4 | 118 | 0.45 | 0.78 | 23 | empty |
| 5 | 73 | 0.37 | 0.77 | 18 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1733 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 890 Ų buried · 12 hydrogen bonds · protein-protein
- A–L · 536 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3MJ9 · Crystal structure of JAML in complex with the stimulatory antibody HL4E10 · the same entry in another collection · chain A against A, TM-score 1.00
- Q80UL9 · AlphaFold monomer V2.0 prediction for junctional adhesion molecule- like (Q80UL9) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q80UL9
- Elsewhere: RCSB PDB 3MJ9 · PDBe 3MJ9 · UniProt Q80UL9
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