MolNFT v1 · #154961 · protein
Crystal structure of the human adiponectin receptor 2
6KS1 · Adiponectin receptor protein 2: “Crystal structure of the human adiponectin receptor 2”. X-ray diffraction, 4 ligands (OLB, OLA, LPX), 7 pockets (best druggability 0.83). MolNFT v1 #154961 on GenesisL1: 3D structure, binding sites…
- PDB
- 6KS1
- Type
- protein
- Length
- 512 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adiponectin receptor protein 2; The heavy chain variable domain (antibody); The light…
- UniProt
- Q86V24
- Ligands
- OLB, OLA, LPX, ZN
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adiponectin receptor protein 2 | protein | 286 | 72% helix, 1% strand | Q86V24 |
| H | The heavy chain variable domain (antibody) | protein | 119 | 8% helix, 48% strand | — |
| L | The light chain variable domain (antibody) | protein | 107 | 3% helix, 52% strand | — |
Ligands and binding sites
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 5 copies · chains A
- OLA · Oleic acid · ligand · chains A
- LPX · (2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate · ligand · chains A, L
- ZN · Zinc ion · metal · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.83 | 0.92 | 53 | OLA |
| 2 | 219 | 0.71 | 0.87 | 39 | empty |
| 3 | 116 | 0.51 | 0.81 | 21 | empty |
| 4 | 171 | 0.48 | 0.76 | 33 | empty |
| 5 | 85 | 0.31 | 0.73 | 24 | empty |
Interfaces
3 interfaces between chains.
- H–L · 802 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 482 Ų buried · 6 hydrogen bonds · protein-protein
- A–H · 468 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
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 6KS1 · PDBe 6KS1 · UniProt Q86V24
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