Research workbench
The crystal structure of the jaa-F11 monoclonal antibody Fab fragment
Analyse The crystal structure of the jaa-F11 monoclonal antibody Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GNM
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jaa-F11 Fab antibody fragment, light chain; Jaa-F11 Fab antibody fragment, heavy chain
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Jaa-F11 Fab antibody fragment, light chain | protein | 217 | 7% helix, 54% strand | — |
| H | Jaa-F11 Fab antibody fragment, heavy chain | protein | 218 | 8% helix, 52% strand | — |
Ligands and binding sites
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 | 807 | 0.68 | 0.75 | 73 | empty |
| 2 | 56 | 0.47 | 0.85 | 19 | empty |
| 3 | 135 | 0.43 | 0.76 | 32 | empty |
| 4 | 85 | 0.38 | 0.76 | 16 | empty |
| 5 | 107 | 0.37 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- L–H · 1870 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3GNM · The crystal structure of the JAA-F11 monoclonal antibody Fab fragment · the same entry in another collection · chain L against L, 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 3GNM · PDBe 3GNM
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