Research workbench
The complex of C4.4A with its antibody 11H10 Fab fragment
Analyse The complex of C4.4A with its antibody 11H10 Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ION
- Type
- protein
- Length
- 606 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-C4.4A antibody 11H10, light chain; Anti-C4.4A antibody 11H10, heavy chain; LY6/PLAUR…
- UniProt
- O95274
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Anti-C4.4A antibody 11H10, light chain | protein | 213 | 6% helix, 55% strand | — |
| H | Anti-C4.4A antibody 11H10, heavy chain | protein | 208 | 6% helix, 54% strand | — |
| A | LY6/PLAUR domain-containing protein 3 | protein | 185 | 5% helix, 50% strand | O95274 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 290 | 0.54 | 0.75 | 37 | empty |
| 2 | 86 | 0.38 | 0.77 | 16 | NAG |
| 3 | 109 | 0.34 | 0.73 | 22 | empty |
| 4 | 83 | 0.33 | 0.74 | 18 | empty |
| 5 | 65 | 0.33 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1761 Ų buried · 17 hydrogen bonds · protein-protein
- H–A · 685 Ų buried · 9 hydrogen bonds · protein-protein
- L–A · 215 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6ION · The complex of C4.4A with its antibody 11H10 Fab fragment · the same entry in another collection · chain A against A, TM-score 1.00
- O95274 · AlphaFold monomer V2.0 prediction for LY6/PLAUR domain-containing protein 3 (O95274) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O95274
- Elsewhere: RCSB PDB 6ION · PDBe 6ION · UniProt O95274
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