Research workbench
Fab of 5.6 monoclonal mouse IGG1 co-crystallized with the trisaccharide form of serotype 3 pneumococcal capsular polysaccharide
Analyse Fab of 5.6 monoclonal mouse IGG1 co-crystallized with the trisaccharide form of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JVD
- Type
- protein
- Length
- 426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5.6 Fab heavy chain; 5.6 Fab light chain
- Ligands
- BGC, BDP
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 5.6 Fab heavy chain | protein | 214 | 4% helix, 52% strand | — |
| L | 5.6 Fab light chain | protein | 212 | 6% helix, 52% strand | — |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains H, L
- BDP · beta-D-glucopyranuronic acid · sugar · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.65 | 0.76 | 63 | empty |
| 2 | 62 | 0.50 | 0.86 | 22 | empty |
| 3 | 81 | 0.33 | 0.74 | 20 | empty |
| 4 | 72 | 0.31 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- H–L · 1785 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7JVD · Fab of 5.6 monoclonal mouse IgG1 co-crystallized with the trisaccharide form of serotype… · 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 7JVD · PDBe 7JVD
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