Research workbench
Novel non-antibody protein scaffold targeting CD40L
Analyse Novel non-antibody protein scaffold targeting CD40L in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BRB
- Type
- protein
- Length
- 229 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD40 ligand; TN3-like
- UniProt
- P29965
- Ligands
- NAG, BMA
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CD40 ligand | protein | 142 | 2% helix, 53% strand | P29965 |
| D | TN3-like | protein | 87 | 3% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.53 | 0.79 | 30 | empty |
| 2 | 161 | 0.47 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–D · 581 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P29965
- Elsewhere: RCSB PDB 6BRB · PDBe 6BRB · UniProt P29965
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