Research workbench
Crystal structure of extracellular domains of mouse rank-rankl complex
Analyse Crystal structure of extracellular domains of mouse rank-rankl complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QBQ
- Type
- protein
- Length
- 638 residues
- Chains
- 4
- 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
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tumor necrosis factor ligand superfamily member 11 | protein | 155 | 4% helix, 55% strand | O35235 |
| B, D | Tumor necrosis factor receptor superfamily member 11A | protein | 164 | 4% helix, 35% strand | O35305 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.56 | 0.77 | 35 | empty |
| 2 | 152 | 0.46 | 0.76 | 33 | empty |
| 3 | 151 | 0.44 | 0.75 | 33 | empty |
| 4 | 123 | 0.42 | 0.76 | 24 | empty |
| 5 | 52 | 0.34 | 0.79 | 18 | empty |
Interfaces
4 interfaces between chains.
- C–D · 822 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 767 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 316 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 101 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 3QBQ · Crystal structure of extracellular domains of mouse RANK-RANKL complex · the same entry in another collection · chain A against A, TM-score 1.00
- O35305 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain B against A, TM-score 0.98
- 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 0.97
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 3QBQ · PDBe 3QBQ · UniProt O35235 · UniProt O35305
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.