MolNFT v1 · #79925 · protein
Crystal structure of fas receptor extracellular domain in complex with Fab EP6B_B01
3THM · Fab EP6B_B01, light chain: “Crystal structure of fas receptor extracellular domain in complex with Fab EP6B_B01”. X-ray diffraction, 2 ligands (NAG, FUC), 4 pockets (best druggability 0.67). MolNFT v1 #79925 on GenesisL1: 3D…
- PDB
- 3THM
- Type
- protein
- Length
- 519 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab EP6B_B01, light chain; Fab EP6B_B01, heavy chain; Tumor necrosis factor receptor…
- UniProt
- P25445
- Ligands
- NAG, FUC
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab EP6B_B01, light chain | protein | 214 | 6% helix, 50% strand | — |
| H | Fab EP6B_B01, heavy chain | protein | 228 | 8% helix, 56% strand | — |
| F | Tumor necrosis factor receptor superfamily member 6 | protein | 77 | 0% helix, 27% strand | P25445 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains L
- FUC · alpha-L-fucopyranose · sugar · chains L
- 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.67 | 0.74 | 77 | EDO |
| 2 | 157 | 0.45 | 0.75 | 29 | empty |
| 3 | 76 | 0.42 | 0.80 | 16 | empty |
| 4 | 67 | 0.33 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1890 Ų buried · 14 hydrogen bonds · protein-protein
- H–F · 827 Ų buried · 12 hydrogen bonds · protein-protein
- L–F · 340 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3THM · Crystal structure of Fas receptor extracellular domain in complex with Fab EP6b_B01 · 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 0.94
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 3THM · PDBe 3THM · UniProt P25445
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