Research workbench
Crystal structure of a catalytic antibody with a serine protease active site
Analyse Crystal structure of a catalytic antibody with a serine protease active site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EAP
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG2B-kappa 17E8 Fab (light chain); IGG2B-kappa 17E8 Fab (heavy chain)
- Ligands
- HEP
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | IGG2B-kappa 17E8 Fab (light chain) | protein | 213 | 5% helix, 49% strand | — |
| B | IGG2B-kappa 17E8 Fab (heavy chain) | protein | 216 | 7% helix, 49% strand | — |
Ligands and binding sites
- HEP · Phenyl[1-(N-succinylamino)pentyl]phosphonate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.65 | 0.86 | 24 | HEP |
| 2 | 247 | 0.55 | 0.77 | 45 | empty |
| 3 | 233 | 0.49 | 0.75 | 35 | empty |
| 4 | 108 | 0.36 | 0.74 | 19 | empty |
| 5 | 94 | 0.32 | 0.72 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1860 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1EAP · Crystal structure of a catalytic antibody with a serine protease active site · 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 1EAP · PDBe 1EAP
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