Research workbench
Crystal structure of 4-1BB in complex with a vhh
Analyse Crystal structure of 4-1BB in complex with a vhh in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D4B
- Type
- protein
- Length
- 265 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor receptor superfamily member 9; Anti-4-1BB vhh
- UniProt
- Q07011
- Ligands
- NAG, MAN, FUC, BMA, CL, SO4
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor receptor superfamily member 9 | protein | 139 | 4% helix, 30% strand | Q07011 |
| B | Anti-4-1BB vhh | protein | 126 | 7% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- CL · Chloride ion · ion · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 724 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7D4B · Crystal structure of 4-1BB in complex with a VHH · the same entry in another collection · chain A against A, TM-score 1.00
- Q07011 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member 9… · a predicted model of the same protein · chain A against A, TM-score 0.67
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 Q07011
- Elsewhere: RCSB PDB 7D4B · PDBe 7D4B · UniProt Q07011
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