MolNFT v1 · #79988 · protein
Crystal structure of fas receptor extracellular domain in complex with Fab E09
3TJE · Fab E09, light chain: “Crystal structure of fas receptor extracellular domain in complex with Fab E09”. X-ray diffraction, 2 ligands (CD, CL), 5 pockets (best druggability 0.67). MolNFT v1 #79988 on GenesisL1: 3D structure, binding…
- 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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