MolNFT v1 · #28020 · protein
Fab fragment of catalytic elimination antibody 34E4 E(H50)D mutant in complex with hapten
1Y18 · Catalytic antibody 34E4 light chain: “Fab fragment of catalytic elimination antibody 34E4 E(H50)D mutant in complex with hapten”. X-ray diffraction, 2 ligands (HAN, CL), 20 pockets (best druggability 0.82). MolNFT v1 #28020 on…
- PDB
- 1Y18
- Type
- protein
- Length
- 1,768 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalytic antibody 34E4 light chain; Catalytic antibody 34E4 heavy chain
- Ligands
- HAN, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A, C, E | Catalytic antibody 34E4 light chain | protein | 216 | 7% helix, 52% strand | — |
| H, B, D, F | Catalytic antibody 34E4 heavy chain | protein | 226 | 9% helix, 53% strand | — |
Ligands and binding sites
- HAN · 2-amino-5,6-dimethyl-benzimidazole-1-pentanoic acid · ligand · 4 copies · chains L, H, A, B, C, D, E, F
- CL · Chloride ion · ion · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.82 | 0.84 | 110 | empty |
| 2 | 1152 | 0.78 | 0.80 | 119 | empty |
| 3 | 830 | 0.77 | 0.81 | 84 | empty |
| 4 | 1007 | 0.76 | 0.79 | 113 | empty |
| 5 | 781 | 0.75 | 0.80 | 98 | empty |
Interfaces
17 interfaces between chains.
- C–D · 2017 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1962 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1921 Ų buried · 14 hydrogen bonds · protein-protein
- L–H · 1896 Ų buried · 11 hydrogen bonds · protein-protein
- H–B · 1047 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 1Y18 · Fab fragment of catalytic elimination antibody 34E4 E(H50)D mutant in complex with hapten · 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 1Y18 · PDBe 1Y18
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