Research workbench
Crystal structure of human adiponectin receptor 2 in complex with a C18 free fatty acid at 2.4 ångström resolution
Analyse Crystal structure of human adiponectin receptor 2 in complex with a C18 free… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LX9
- Type
- protein
- Length
- 511 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human adiponectin receptor 2; Single-chain variable fragment
- Ligands
- OLB, OLA, ZN
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human adiponectin receptor 2 | protein | 283 | 73% helix, 1% strand | — |
| H | Single-chain variable fragment | protein | 228 | 5% helix, 49% strand | — |
Ligands and binding sites
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 12 copies · chains A, H
- OLA · Oleic acid · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.85 | 0.90 | 76 | ZN, OLA, OLB |
| 2 | 166 | 0.48 | 0.77 | 37 | empty |
| 3 | 87 | 0.44 | 0.80 | 16 | empty |
| 4 | 98 | 0.34 | 0.73 | 21 | empty |
| 5 | 77 | 0.32 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–H · 899 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5LX9 · Crystal structure of human adiponectin receptor 2 in complex with a C18 free fatty acid… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5LX9 · PDBe 5LX9
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