MolNFT v1 · #171224 · protein
Cryogenic human adiponectin receptor 2 (ADIPOR2) with tb-XO4 ligand determined by serial crystallography (ssx) using crystaldirect
6YXG · Adiponectin receptor protein 2: “Cryogenic human adiponectin receptor 2 (ADIPOR2) with tb-XO4 ligand determined by serial crystallography…”. X-ray diffraction, 4 ligands (OLB, 7MT, OLA), 6 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 6YXG
- Type
- protein
- Length
- 519 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adiponectin receptor protein 2; V region heavy and light chains
- UniProt
- Q86V24
- Ligands
- OLB, 7MT, OLA, ZN
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adiponectin receptor protein 2 | protein | 283 | 73% helix, 1% strand | Q86V24 |
| H | V region heavy and light chains | protein | 236 | 6% helix, 47% strand | — |
Ligands and binding sites
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 10 copies · chains A, H
- 7MT · Tb-Xo4 · ligand · 2 copies · chains 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
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 | 558 | 0.86 | 0.91 | 74 | OLA, OLB |
| 2 | 277 | 0.55 | 0.77 | 31 | empty |
| 3 | 162 | 0.46 | 0.76 | 31 | empty |
| 4 | 111 | 0.45 | 0.78 | 17 | empty |
| 5 | 78 | 0.35 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–H · 880 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6YXG · Cryogenic human adiponectin receptor 2 (ADIPOR2) with Tb-XO4 ligand 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 6YXG · PDBe 6YXG · UniProt Q86V24
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