Research workbench
Crystal structure of cocaine catalytic antibody 7A1 Fab' in complex with ecgonine methyl ester and benzoic acid
Analyse Crystal structure of cocaine catalytic antibody 7A1 Fab' 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
- 2AJY
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody 7A1 Fab'
- Ligands
- ECG, BEZ, ZN
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antibody 7A1 Fab' | protein | 216 | 6% helix, 50% strand | — |
| H | Antibody 7A1 Fab' | protein | 219 | 7% helix, 51% strand | — |
Ligands and binding sites
- ECG · 3-hydroxy-8-methyl-8-aza-bicyclo[3.2.1]octane-2-carboxylic acid methyl ester · ligand · chains L, H
- BEZ · Benzoic acid · ligand · chains H
- ZN · Zinc ion · metal · 5 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.66 | 0.75 | 69 | ZN |
| 2 | 59 | 0.52 | 0.87 | 21 | empty |
| 3 | 176 | 0.49 | 0.76 | 26 | empty |
| 4 | 130 | 0.48 | 0.78 | 19 | ECG, BEZ |
Interfaces
1 interface between chains.
- L–H · 1955 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2AJY · Crystal Structure of Cocaine catalytic Antibody 7A1 Fab' in Complex with ecgonine methyl… · 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 2AJY · PDBe 2AJY
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