Research workbench
Crystal structure of murine 4-1BB from HEK293T cells in P21212 space group
Analyse Crystal structure of murine 4-1BB from HEK293T cells in P21212 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WJF
- Type
- protein
- Length
- 269 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor receptor superfamily member 9
- UniProt
- P20334
- Ligands
- NAG
- Pockets
- 1 · best druggability 0.26
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor receptor superfamily member 9 | protein | 135 | 4% helix, 36% strand | P20334 |
| B | Tumor necrosis factor receptor superfamily member 9 | protein | 134 | 0% helix, 32% strand | P20334 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
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 | 59 | 0.26 | 0.72 | 15 | EDO |
Interfaces
1 interface between chains.
- A–B · 206 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5WJF · Crystal structure of murine 4-1BB from HEK293T cells in P21212 space group · the same entry in another collection · chain A against A, TM-score 1.00
- P20334 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member 9… · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P20334
- Elsewhere: RCSB PDB 5WJF · PDBe 5WJF · UniProt P20334
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