Research workbench
Crystal structure of hapten complex of catalytic elimination antibody 13G5 (GLU(L39)GLN 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
- 3FO2
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalytic antibody Fab 13G5 kappa light chain chimera; Catalytic antibody Fab 13G5 IGG2B…
- Ligands
- BZH
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Catalytic antibody Fab 13G5 kappa light chain chimera | protein | 216 | 5% helix, 52% strand | — |
| H, B | Catalytic antibody Fab 13G5 IGG2B heavy chain chimera | protein | 214 | 7% helix, 52% 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 | 681 | 0.79 | 0.83 | 93 | empty |
| 2 | 270 | 0.67 | 0.83 | 38 | empty |
| 3 | 68 | 0.57 | 0.88 | 21 | BZH |
| 4 | 59 | 0.55 | 0.88 | 20 | BZH |
| 5 | 76 | 0.54 | 0.87 | 22 | empty |
Interfaces
6 interfaces between chains.
- L–H · 1776 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1773 Ų buried · 15 hydrogen bonds · protein-protein
- H–B · 515 Ų buried · 4 hydrogen bonds · protein-protein
- L–A · 403 Ų buried · 3 hydrogen bonds · protein-protein
- H–A · 40 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3FO2 · Crystal structure of hapten complex of catalytic elimination antibody 13G5 (Glu(L39)Gln… · 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
- Elsewhere: RCSB PDB 3FO2 · PDBe 3FO2
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