MolNFT v1 · #92770 · protein
Crystal structure of mouse rank bound to rankl
4GIQ · Tumor necrosis factor ligand superfamily member 11: “Crystal structure of mouse rank bound to rankl”. X-ray diffraction, 3 ligands (NAG, NA, CL), 2 pockets (best druggability 0.43). MolNFT v1 #92770 on GenesisL1: 3D structure…
- PDB
- 4GIQ
- Type
- protein
- Length
- 319 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor ligand superfamily member 11; Tumor necrosis factor receptor…
- UniProt
- O35235, O35305
- Ligands
- NAG, NA, CL
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor ligand superfamily member 11 | protein | 155 | 4% helix, 57% strand | O35235 |
| R | Tumor necrosis factor receptor superfamily member 11A | protein | 164 | 4% helix, 36% strand | O35305 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains R
- NA · Sodium ion · metal · chains R
- CL · Chloride ion · ion · 2 copies · chains A, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.43 | 0.75 | 29 | empty |
| 2 | 60 | 0.29 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–R · 812 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4GIQ · Crystal Structure of mouse RANK bound to RANKL · the same entry in another collection · chain A against A, TM-score 1.00
- O35235 · 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 0.98
- O35305 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain R 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 O35235
- Every structure of UniProt O35305
- Elsewhere: RCSB PDB 4GIQ · PDBe 4GIQ · UniProt O35235 · UniProt O35305
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