MolNFT v1 · #171223 · protein
Cryogenic human adiponectin receptor 2 (ADIPOR2) with gd-DO3 ligand determined by serial crystallography (ssx) using crystaldirect
6YXF · Adiponectin receptor protein 2: “Cryogenic human adiponectin receptor 2 (ADIPOR2) with gd-DO3 ligand determined by serial crystallography…”. X-ray diffraction, 5 ligands (OLB, DO3, OLA), 5 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 6YXF
- Type
- protein
- Length
- 511 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, DO3, OLA, GD, ZN
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adiponectin receptor protein 2 | protein | 283 | 72% helix, 1% strand | Q86V24 |
| H | V region heavy and light chains | protein | 228 | 5% helix, 47% strand | — |
Ligands and binding sites
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 6 copies · chains A, H
- DO3 · 10-((2R)-2-hydroxypropyl)-1,4,7,10-tetraazacyclododecane 1,4,7-triacetic acid · ligand · 3 copies · chains A, H
- OLA · Oleic acid · ligand · chains A
- GD · Gadolinium atom · metal · 3 copies · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 534 | 0.85 | 0.91 | 68 | ZN, OLA, OLB |
| 2 | 148 | 0.48 | 0.77 | 23 | empty |
| 3 | 140 | 0.44 | 0.76 | 28 | empty |
| 4 | 72 | 0.32 | 0.75 | 17 | empty |
| 5 | 76 | 0.31 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–H · 891 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6YXF · Cryogenic human adiponectin receptor 2 (ADIPOR2) with Gd-DO3 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 6YXF · PDBe 6YXF · UniProt Q86V24
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