Research workbench
Crystal structure of a chimeric antigen receptor (car) scfv domain rearrangement forming a vl-vl dimer
Analyse Crystal structure of a chimeric antigen receptor (car) scfv domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JO8
- Type
- protein
- Length
- 217 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 47G4-CD828Z
- Pockets
- 3 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 47G4-CD828Z | protein | 107 | 6% helix, 50% strand | — |
| B | 47G4-CD828Z | protein | 110 | 5% helix, 48% strand | — |
Ligands and binding sites
- 1PE · Pentaethylene glycol · additive · chains A, B
- MLI · Malonate ion · additive · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.39 | 0.76 | 17 | empty |
| 2 | 77 | 0.39 | 0.78 | 20 | 1PE |
| 3 | 82 | 0.38 | 0.77 | 19 | PG4 |
Interfaces
1 interface between chains.
- A–B · 739 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7JO8 · Crystal structure of a Chimeric Antigen Receptor (CAR) scFv domain rearrangement forming… · the same entry in another collection · chain A against A, 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 7JO8 · PDBe 7JO8
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