MolNFT v1 · #31114 · protein
Crystal structure of cocaine catalytic antibody 7A1 Fab' in complex with ecgonine methyl ester and benzoic acid
2AJY: “Crystal structure of cocaine catalytic antibody 7A1 Fab' in complex with ecgonine methyl ester and benzoic…”. X-ray diffraction, 3 ligands (ECG, BEZ, ZN), 4 pockets (best druggability 0.66). MolNFT v1 #31114 on GenesisL1: 3D…
- 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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