Research workbench
Crystal structure of an anti-carbohydrate antibody directed against vibrio cholerae O1 in complex with antigen
Analyse Crystal structure of an anti-carbohydrate antibody directed against vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F4Y
- Type
- protein
- Length
- 426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody S-20-4, Fab fragment, light chain; Antibody S-20-4, Fab fragment, heavy chain
- Ligands
- ZD0, ZCZ
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antibody S-20-4, Fab fragment, light chain | protein | 210 | 7% helix, 49% strand | — |
| H | Antibody S-20-4, Fab fragment, heavy chain | protein | 216 | 1% helix, 51% strand | — |
Ligands and binding sites
- ZD0 · methyl 4,6-dideoxy-4-{[(2R)-2,4-dihydroxybutanoyl]amino}-alpha-D-mannopyranoside · ligand · chains L
- ZCZ · 4,6-dideoxy-4-{[(2R)-2,4-dihydroxybutanoyl]amino}-2-O-methyl-alpha-D-mannopyranose · ligand · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.67 | 0.76 | 63 | empty |
| 2 | 231 | 0.53 | 0.77 | 31 | empty |
| 3 | 54 | 0.36 | 0.79 | 16 | empty |
| 4 | 88 | 0.36 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- L–H · 1854 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1F4Y · Crystal structure of an anti-carbohydrate antibody directed against vibrio cholerae O1 in… · 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 1F4Y · PDBe 1F4Y
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