Research workbench
Crystal structure of a diels-alderase catalytic antibody 1E9 in complex with its hapten
Analyse Crystal structure of a diels-alderase catalytic antibody 1E9 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C1E
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalytic antibody 1E9 (light chain); Catalytic antibody 1E9 (heavy chain)
- Ligands
- MLT, ENH
- Pockets
- 7 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Catalytic antibody 1E9 (light chain) | protein | 216 | 6% helix, 51% strand | — |
| H | Catalytic antibody 1E9 (heavy chain) | protein | 219 | 8% helix, 52% strand | — |
Ligands and binding sites
- MLT · D-malate · ligand · chains L
- ENH · 1,7,8,9,10,10-hexachloro-4-methyl-4-aza-tricyclo[5.2.1.0(2,6)]dec-8-ene-3,5-dione · ligand · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.57 | 0.82 | 24 | ENH |
| 2 | 148 | 0.53 | 0.80 | 21 | empty |
| 3 | 197 | 0.45 | 0.74 | 32 | empty |
| 4 | 93 | 0.36 | 0.75 | 24 | empty |
| 5 | 88 | 0.36 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- L–H · 1834 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1C1E · Crystal structure of a diels-alderase catalytic antibody 1E9 in complex with its 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 1C1E · PDBe 1C1E
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