Research workbench
Crystal structure of the Fab fragment of anti-ciguatoxin antibody 10C9 in complex with CTX3C_ABCDE
Analyse Crystal structure of the Fab fragment of anti-ciguatoxin antibody 10C9 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z92
- Type
- protein
- Length
- 416 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-ciguatoxin antibody 10C9 Fab heavy chain; Anti-ciguatoxin antibody 10C9 Fab light…
- Ligands
- ENE
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anti-ciguatoxin antibody 10C9 Fab heavy chain | protein | 206 | 4% helix, 55% strand | — |
| B | Anti-ciguatoxin antibody 10C9 Fab light chain | protein | 210 | 5% helix, 53% strand | — |
Ligands and binding sites
- ENE · (4Z)-2,8:7,12:11,15:14,18:17,22-pentaanhydro-4,5,6,9,10,13,19,20,21-nonadeoxy-D-arabino-D-allo-D-allo-docosa-4,9,20-trienitol · ligand · chains A, B
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.63 | 0.75 | 66 | empty |
| 2 | 147 | 0.60 | 0.83 | 22 | ENE |
| 3 | 66 | 0.38 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1777 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2Z92 · Crystal structure of the Fab fragment of anti-ciguatoxin antibody 10C9 in complex with… · the same entry in another collection · chain A against A, 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 2Z92 · PDBe 2Z92
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