Research workbench
LL2 Fab in complex with anti-kappa vhh domain
Analyse LL2 Fab in complex with anti-kappa vhh domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ANA
- Type
- protein
- Length
- 545 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti kappa vhh domain; LL2 Fab heavy chain; LL2 Fab light chain
- Ligands
- NAG, FUC
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | Anti kappa vhh domain | protein | 120 | 8% helix, 49% strand | — |
| H | LL2 Fab heavy chain | protein | 208 | 10% helix, 53% strand | — |
| L | LL2 Fab light chain | protein | 217 | 6% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains L
- FUC · alpha-L-fucopyranose · sugar · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.77 | 0.84 | 94 | empty |
| 2 | 96 | 0.50 | 0.83 | 27 | empty |
| 3 | 137 | 0.48 | 0.78 | 24 | empty |
| 4 | 194 | 0.47 | 0.75 | 32 | empty |
| 5 | 86 | 0.31 | 0.73 | 17 | empty |
Interfaces
2 interfaces between chains.
- H–L · 1676 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 571 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6ANA · LL2 Fab in complex with anti-Kappa VHH domain · the same entry in another collection · chain K against K, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6ANA · PDBe 6ANA
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