MolNFT v1 · #95982 · protein
Crystal structure of light and DCR3 complex
4J6G · Tumor necrosis factor ligand superfamily member 14: “Crystal structure of light and DCR3 complex”. X-ray diffraction, 5 ligands (NAG, BMA, MAN), 3 pockets (best druggability 0.52). MolNFT v1 #95982 on GenesisL1: 3D structure…
- PDB
- 4J6G
- Type
- protein
- Length
- 603 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor ligand superfamily member 14; Tumor necrosis factor receptor…
- UniProt
- O43557, O95407
- Ligands
- NAG, BMA, MAN, MG, CL
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 1% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tumor necrosis factor ligand superfamily member 14 | protein | 139 | 2% helix, 54% strand | O43557 |
| C | Tumor necrosis factor receptor superfamily member 6B | protein | 163 | 0% helix, 42% strand | O95407 |
| D | Tumor necrosis factor receptor superfamily member 6B | protein | 162 | 2% helix, 42% strand | O95407 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains C, D
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- MG · Magnesium ion · metal · 2 copies · chains C, D
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.52 | 0.78 | 24 | empty |
| 2 | 65 | 0.43 | 0.82 | 21 | empty |
| 3 | 118 | 0.41 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–D · 556 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 539 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 322 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4J6G · CRYSTAL STRUCTURE OF LIGHT AND DcR3 COMPLEX · the same entry in another collection · chain A against A, TM-score 1.00
- O43557 · AlphaFold monomer V2.0 prediction for tumor necrosis factor ligand superfamily member 14… · a predicted model of the same protein · chain A against A, TM-score 0.98
- O95407 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain D against A, TM-score 0.96
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 O43557
- Every structure of UniProt O95407
- Elsewhere: RCSB PDB 4J6G · PDBe 4J6G · UniProt O43557 · UniProt O95407
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.