Research workbench
Crystal structure of fas receptor extracellular domain in complex with Fab E09
Analyse Crystal structure of fas receptor extracellular domain in complex with Fab E09 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TJE
- Type
- protein
- Length
- 542 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab E09, light chain; Fab E09, heavy chain; Tumor necrosis factor receptor superfamily…
- UniProt
- P25445
- Ligands
- CD, CL
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab E09, light chain | protein | 213 | 7% helix, 51% strand | — |
| H | Fab E09, heavy chain | protein | 229 | 8% helix, 55% strand | — |
| F | Tumor necrosis factor receptor superfamily member 6 | protein | 100 | 3% helix, 27% strand | P25445 |
Ligands and binding sites
- CD · Cadmium ion · metal · 2 copies · chains F
- CL · Chloride ion · ion · chains L, F
- EDO · 1,2-ethanediol · additive · 5 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.67 | 0.75 | 70 | EDO |
| 2 | 66 | 0.40 | 0.80 | 22 | empty |
| 3 | 60 | 0.40 | 0.81 | 15 | empty |
| 4 | 54 | 0.32 | 0.77 | 16 | empty |
| 5 | 71 | 0.31 | 0.74 | 21 | EDO |
Interfaces
3 interfaces between chains.
- L–H · 1899 Ų buried · 12 hydrogen bonds · protein-protein
- H–F · 807 Ų buried · 12 hydrogen bonds · protein-protein
- L–F · 326 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3TJE · Crystal structure of Fas receptor extracellular domain in complex with Fab E09 · the same entry in another collection · chain L against L, TM-score 1.00
- P25445 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member 6… · a predicted model of the same protein · chain F 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 P25445
- Elsewhere: RCSB PDB 3TJE · PDBe 3TJE · UniProt P25445
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