Research workbench
Structure of the anti-cholera toxin antibody Fab fragment TE33 in complex with a D-peptide
Analyse Structure of the anti-cholera toxin antibody Fab fragment TE33 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZEA
- Type
- protein
- Length
- 434 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monoclonal anti-cholera toxin IGG1 kappa antibody, L chain; Monoclonal anti-cholera toxin…
- UniProt
- A2NHM3, Q921A6
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Monoclonal anti-cholera toxin IGG1 kappa antibody, L chain | protein | 216 | 6% helix, 52% strand | A2NHM3 |
| H | Monoclonal anti-cholera toxin IGG1 kappa antibody, H chain | protein | 209 | 10% helix, 54% strand | Q921A6 |
| A | Short synthetic D-amino acid peptide D2 | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- CIT · Citric acid · additive · 2 copies · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.49 | 0.74 | 36 | empty |
| 2 | 114 | 0.37 | 0.74 | 18 | empty |
| 3 | 56 | 0.34 | 0.78 | 18 | empty |
| 4 | 77 | 0.30 | 0.73 | 22 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1755 Ų buried · 15 hydrogen bonds · protein-protein
- H–A · 443 Ų buried · 9 hydrogen bonds · protein-protein
- L–A · 147 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 d-amino, 4 disulfide (D-amino acid, disulfide).
Compared structures
- 1ZEA · Structure of the anti-cholera toxin antibody Fab fragment TE33 in complex with a D-peptide · 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
- Every structure of UniProt A2NHM3
- Every structure of UniProt Q921A6
- Elsewhere: RCSB PDB 1ZEA · PDBe 1ZEA · UniProt A2NHM3 · UniProt Q921A6
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