Research workbench
Crystal structure of hapten complex of catalytic elimination antibody 13G5 (Glu(L39)Ala mutant)
Analyse Crystal structure of hapten complex of catalytic elimination antibody 13G5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FO1
- Type
- protein
- Length
- 862 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Mus musculus, Homo sapiens
- Molecule
- Catalytic antibody Fab 13G5 kappa light chain chimera; Catalytic antibody Fab 13G5 IgG2b…
- Ligands
- BZH
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.2 · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Catalytic antibody Fab 13G5 kappa light chain chimera | protein | 216 | 6% helix, 52% strand | — |
| H | Catalytic antibody Fab 13G5 IgG2b heavy chain chimera | protein | 216 | 6% helix, 51% strand | — |
| B | Catalytic antibody Fab 13G5 IgG2b heavy chain chimera | protein | 214 | 7% helix, 51% strand | — |
Ligands and binding sites
- BZH · 5-[(2-amino-1H-benzimidazol-6-yl)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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.75 | 0.83 | 60 | empty |
| 2 | 353 | 0.69 | 0.82 | 48 | empty |
| 3 | 92 | 0.64 | 0.90 | 23 | BZH |
| 4 | 53 | 0.63 | 0.94 | 16 | empty |
| 5 | 85 | 0.61 | 0.88 | 24 | BZH |
Interfaces
6 interfaces between chains.
- L–H · 1861 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1818 Ų buried · 16 hydrogen bonds · protein-protein
- H–B · 488 Ų buried · 5 hydrogen bonds · protein-protein
- L–A · 272 Ų buried · 1 hydrogen bond · protein-protein
- L–B · 38 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3FO1 · Crystal structure of hapten complex of catalytic elimination antibody 13G5 (GLU(L39)ALA… · 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 3FO1 · PDBe 3FO1
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