Research workbench
Crystal structure of aldolase antibody 33F12 Fab' in complex with hapten 1,3-diketone
Analyse Crystal structure of aldolase antibody 33F12 Fab' in complex with hapten… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FO9
- Type
- protein
- Length
- 874 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Mus musculus
- Molecule
- Immunoglobulin IGG2A - light chain; Immunoglobulin IGG2A - heavy chain
- Ligands
- DIK
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.9 · 2 distinct chains · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Immunoglobulin IGG2A - light chain | protein | 219 | 5% helix, 54% strand | — |
| H, B | Immunoglobulin IGG2A - heavy chain | protein | 218 | 8% helix, 54% strand | — |
Ligands and binding sites
- DIK · 5-{[4-(5-methyl-3-oxohex-4-en-1-yl)phenyl]amino}-5-oxopentanoic acid · ligand · 2 copies · chains L, H, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.77 | 0.80 | 113 | empty |
| 2 | 937 | 0.70 | 0.75 | 97 | empty |
| 3 | 182 | 0.67 | 0.86 | 29 | DIK |
| 4 | 168 | 0.64 | 0.85 | 29 | DIK |
| 5 | 74 | 0.54 | 0.87 | 23 | empty |
Interfaces
4 interfaces between chains.
- L–H · 1839 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1763 Ų buried · 16 hydrogen bonds · protein-protein
- H–A · 566 Ų buried · 6 hydrogen bonds · protein-protein
- H–B · 449 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 3FO9 · Crystal structure of aldolase antibody 33F12 Fab' in complex with hapten 1,3-diketone · 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 3FO9 · PDBe 3FO9
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