Research workbench
Cryogenic human adiponectin receptor 2 (ADIPOR2) at 2.4 a resolution determined by serial crystallography (ssx) using crystaldirect
Analyse Cryogenic human adiponectin receptor 2 (ADIPOR2) at 2.4 a resolution determined… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YX9
- Type
- protein
- Length
- 514 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adiponectin receptor protein 2; V region heavy chain; V region light chain
- UniProt
- Q86V24
- Ligands
- OLB, OLA, ZN
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adiponectin receptor protein 2 | protein | 285 | 73% helix, 1% strand | Q86V24 |
| H | V region heavy chain | protein | 121 | 10% helix, 47% strand | — |
| L | V region light chain | protein | 108 | 3% helix, 51% strand | — |
Ligands and binding sites
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 5 copies · chains A, L
- OLA · Oleic acid · ligand · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.85 | 0.91 | 75 | ZN, OLB, OLA |
| 2 | 265 | 0.54 | 0.76 | 50 | empty |
| 3 | 105 | 0.48 | 0.80 | 22 | empty |
| 4 | 92 | 0.36 | 0.75 | 21 | empty |
| 5 | 83 | 0.31 | 0.73 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 794 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 503 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 477 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6YX9 · Cryogenic human adiponectin receptor 2 (ADIPOR2) at 2.4 A resolution determined by Serial… · the same entry in another collection · chain A against A, TM-score 1.00
- Q86V24 · AlphaFold monomer V2.0 prediction for adiponectin receptor protein 2 (Q86V24) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q86V24
- Elsewhere: RCSB PDB 6YX9 · PDBe 6YX9 · UniProt Q86V24
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