MolNFT v1 · #3037 · protein
Convergence of catalytic antibody and terpene cyclase mechanisms: polyene cyclization directed by carbocation-pi interactions
1CF8 · Protein (catalytic antibody 19A4 (light chain)): “Convergence of catalytic antibody and terpene cyclase mechanisms: polyene cyclization directed by…”. X-ray diffraction, 2 ligands (HAZ, CD), 4 pockets (best druggability 0.71).…
- PDB
- 1CF8
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (catalytic antibody 19A4 (light chain)); Protein (catalytic antibody 19A4 (heavy…
- Ligands
- HAZ, CD
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Protein (catalytic antibody 19A4 (light chain)) | protein | 215 | 7% helix, 52% strand | — |
| H | Protein (catalytic antibody 19A4 (heavy chain)) | protein | 218 | 4% helix, 53% strand | — |
Ligands and binding sites
- HAZ · 4-{4-[2-(1A,7A-dimethyl-4-oxy-octahydro-1-oxa-4-aza-cyclopropa[a]naphthalen-4-yl) -acetylamino]-phenylcarbamoyl}-butyric acid · ligand · chains L, H
- CD · Cadmium ion · metal · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.71 | 0.90 | 21 | HAZ |
| 2 | 227 | 0.55 | 0.78 | 31 | CD |
| 3 | 319 | 0.54 | 0.75 | 45 | empty |
| 4 | 65 | 0.29 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- L–H · 1857 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1CF8 · Convergence of catalytic antibody and terpene cyclase mechanisms: polyene cyclization… · 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 1CF8 · PDBe 1CF8
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