Research workbench
Crystal structure of the Fab fragment of a glycosylated lymphoma antibody
Analyse Crystal structure of the Fab fragment of a glycosylated lymphoma antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ARN
- Type
- protein
- Length
- 438 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab fragment heavy chain; Antibody Fab fragment light chain
- Ligands
- NAG, BMA, MAN
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody Fab fragment heavy chain | protein | 222 | 8% helix, 50% strand | — |
| L | Antibody Fab fragment light chain | protein | 216 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains H, L
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains L
- GOL · Glycerol · additive · 3 copies · chains H, L
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 | 675 | 0.66 | 0.75 | 62 | empty |
| 2 | 54 | 0.50 | 0.87 | 22 | GOL |
| 3 | 71 | 0.34 | 0.76 | 20 | empty |
| 4 | 73 | 0.33 | 0.75 | 22 | empty |
| 5 | 74 | 0.32 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- H–L · 1762 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7ARN · Crystal Structure of the Fab Fragment of a Glycosylated Lymphoma Antibody · the same entry in another collection · chain H against H, 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 7ARN · PDBe 7ARN
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