Research workbench
Crystal structure of murine 4-1BB from HEK293T cells in P21 space group
Analyse Crystal structure of murine 4-1BB from HEK293T cells in P21 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WI8
- Type
- protein
- Length
- 539 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor receptor superfamily member 9
- UniProt
- P20334
- Ligands
- NAG, BMA, FUC, MAN
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor receptor superfamily member 9 | protein | 136 | 2% helix, 32% strand | P20334 |
| B | Tumor necrosis factor receptor superfamily member 9 | protein | 135 | 5% helix, 29% strand | P20334 |
| C, D | Tumor necrosis factor receptor superfamily member 9 | protein | 134 | 2% helix, 32% strand | P20334 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B, D
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
- GOL · Glycerol · additive · 9 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, C, B, D
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 | 351 | 0.56 | 0.75 | 44 | EDO |
| 2 | 175 | 0.45 | 0.75 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–C · 475 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 465 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 117 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 107 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 48 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5WI8 · Crystal structure of murine 4-1BB from HEK293T cells in P21 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 A against A, TM-score 0.97
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 5WI8 · PDBe 5WI8 · UniProt P20334
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