MolNFT v1 · #81462 · protein
Human RANKL/OPG complex
3URF · Tumor necrosis factor ligand superfamily member 11, soluble…: “Human RANKL/OPG complex”. X-ray diffraction, 1 ligand (NAG), 2 pockets (best druggability 0.58). MolNFT v1 #81462 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3URF
- Type
- protein
- Length
- 320 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor ligand superfamily member 11, soluble form; Tumor necrosis factor…
- UniProt
- O14788, O00300
- Ligands
- NAG
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor ligand superfamily member 11, soluble form | protein | 156 | 2% helix, 58% strand | O14788 |
| Z | Tumor necrosis factor receptor superfamily member 11B | protein | 164 | 0% helix, 34% strand | O00300 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains Z
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 | 288 | 0.58 | 0.78 | 32 | empty |
| 2 | 267 | 0.50 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–Z · 594 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3URF · Human RANKL/OPG complex · the same entry in another collection · chain A against A, TM-score 1.00
- O14788 · AlphaFold monomer V2.0 prediction for tumor necrosis factor ligand superfamily member 11… · a predicted model of the same protein · chain A against A, TM-score 0.96
- O00300 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain Z against A, TM-score 0.78
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 O14788
- Every structure of UniProt O00300
- Elsewhere: RCSB PDB 3URF · PDBe 3URF · UniProt O14788 · UniProt O00300
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