Research workbench
De novo designed receptor transmembrane domains enhance car-T cytotoxicity and attenuate cytokine release
Analyse De novo designed receptor transmembrane domains enhance car-T cytotoxicity and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W9Z
- Type
- protein
- Length
- 173 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- De novo designed receptor transmembrane domain promp C2.1
- Ligands
- OLB
- Pockets
- 1 · best druggability 0.44
Structure
x-ray diffraction · 3 distinct chains · 93% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | De novo designed receptor transmembrane domain promp C2.1 | protein | 29 | 93% helix, 0% strand | — |
| D | De novo designed receptor transmembrane domain promp C2.1 | protein | 30 | 93% helix, 0% strand | — |
| F | De novo designed receptor transmembrane domain promp C2.1 | protein | 27 | 93% helix, 0% strand | — |
Ligands and binding sites
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 2 copies · chains A, B, F, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.44 | 0.81 | 13 | empty |
Interfaces
11 interfaces between chains.
- A–B · 542 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 534 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 495 Ų buried · 3 hydrogen bonds · protein-protein
- C–F · 473 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 452 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (methylation).
Compared structures
- 6W9Z · De novo designed receptor transmembrane domains enhance CAR-T cytotoxicity and attenuate… · 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 6W9Z · PDBe 6W9Z
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