MolNFT v1 · #114380 · protein
Crystal structure of hrankl-mrank complex
5BNQ · Tumor necrosis factor ligand superfamily member 11: “Crystal structure of hrankl-mrank complex”. X-ray diffraction, 3 ligands (NA, CL, PO4), 2 pockets (best druggability 0.65). MolNFT v1 #114380 on GenesisL1: 3D structure, binding…
- PDB
- 5BNQ
- Type
- protein
- Length
- 322 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
- O14788, O35305
- Ligands
- NA, CL, PO4
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor ligand superfamily member 11 | protein | 156 | 6% helix, 57% strand | O14788 |
| R | Tumor necrosis factor receptor superfamily member 11A | protein | 166 | 4% helix, 36% strand | O35305 |
Ligands and binding sites
- NA · Sodium ion · metal · chains R
- CL · Chloride ion · ion · 8 copies · chains A, R
- PO4 · Phosphate ion · ion · 4 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.65 | 0.77 | 60 | CL, PO4 |
| 2 | 102 | 0.39 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–R · 556 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5BNQ · Crystal structure of hRANKL-mRANK 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 0.99
- 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 O14788
- Every structure of UniProt O35305
- Elsewhere: RCSB PDB 5BNQ · PDBe 5BNQ · UniProt O14788 · UniProt O35305
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