Research workbench
Fab fragment of catalytic elimination antibody 34E4 E(H50)D mutant in complex with hapten
Analyse Fab fragment of catalytic elimination antibody 34E4 E(H50)D mutant in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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