Research workbench
Crystal structure of human adiponectin receptor 2 in complex with a C18 free fatty acid at 3.0 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
- 5LXA
- Type
- protein
- Length
- 522 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adiponectin receptor protein 2; Anti-CD30 moab ki-4 scfv
- UniProt
- Q86V24
- Ligands
- OLA, OLB, ZN
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adiponectin receptor protein 2 | protein | 284 | 73% helix, 1% strand | Q86V24 |
| H | Anti-CD30 moab ki-4 scfv | protein | 238 | 4% helix, 48% strand | — |
Ligands and binding sites
- OLA · Oleic acid · ligand · chains A
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · chains A, H
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.84 | 0.90 | 73 | OLA |
| 2 | 199 | 0.51 | 0.77 | 31 | empty |
| 3 | 109 | 0.50 | 0.81 | 19 | empty |
| 4 | 180 | 0.49 | 0.76 | 33 | empty |
| 5 | 78 | 0.33 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–H · 926 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5LXA · 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
- 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 5LXA · PDBe 5LXA · UniProt Q86V24
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