Research workbench
Purple-fluorescent antibody EP2-25C10 in complex with its stilbene hapten
Analyse Purple-fluorescent antibody EP2-25C10 in complex with its stilbene hapten in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CFD
- Type
- protein
- Length
- 865 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purple-fluorescent antibody EP2-25C10-kappa light chain; Purple-fluorescent antibody…
- Ligands
- SPB
- Pockets
- 16 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | Purple-fluorescent antibody EP2-25C10-kappa light chain | protein | 213 | 6% helix, 51% strand | — |
| H | Purple-fluorescent antibody EP2-25C10-IGG2B heavy chain | protein | 220 | 4% helix, 54% strand | — |
| B | Purple-fluorescent antibody EP2-25C10-IGG2B heavy chain | protein | 219 | 1% helix, 55% strand | — |
Ligands and binding sites
- SPB · 4-(4-styryl-phenylcarbamoyl)-butyric acid · ligand · 2 copies · chains L, H, A, B
- GOL · Glycerol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.62 | 0.89 | 26 | SPB |
| 2 | 96 | 0.61 | 0.88 | 24 | SPB |
| 3 | 363 | 0.57 | 0.75 | 43 | empty |
| 4 | 273 | 0.52 | 0.75 | 36 | empty |
| 5 | 140 | 0.42 | 0.75 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1917 Ų buried · 16 hydrogen bonds · protein-protein
- L–H · 1895 Ų buried · 16 hydrogen bonds · protein-protein
- L–A · 118 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3CFD · Purple-fluorescent antibody EP2-25C10 in complex with its stilbene 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 3CFD · PDBe 3CFD
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