MolNFT v1 · #28447 · protein
Catalytic antibody complex
1YEJ · Protein (ig antibody D2.3 (light chain)): “Catalytic antibody complex”. X-ray diffraction, 2 ligands (PNF, ZN), 3 pockets (best druggability 0.62). MolNFT v1 #28447 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1YEJ
- Type
- protein
- Length
- 441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (ig antibody D2.3 (light chain)); Protein (ig antibody D2.3 (heavy chain))
- Ligands
- PNF, ZN
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Protein (ig antibody D2.3 (light chain)) | protein | 219 | 5% helix, 52% strand | — |
| H | Protein (ig antibody D2.3 (heavy chain)) | protein | 222 | 8% helix, 52% strand | — |
Ligands and binding sites
- PNF · 6-{4-[hydroxy-(4-nitro-phenoxy)-phosphoryl]-butyrylamino}-hexanoic acid · ligand · chains L, H
- ZN · Zinc ion · metal · 7 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.62 | 0.84 | 25 | PNF |
| 2 | 180 | 0.41 | 0.73 | 35 | empty |
| 3 | 62 | 0.35 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- L–H · 2080 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1YEJ · Catalytic antibody complex · 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 1YEJ · PDBe 1YEJ
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