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Crystal structure of the human adiponectin receptor 1

Analyse Crystal structure of the human adiponectin receptor 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KS0
Type: protein
Length: 512 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adiponectin receptor protein 1; The heavy chain variable domain (antibody); The light…
UniProt: Q96A54
Ligands: ZN, PO4
Pockets: 4 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adiponectin receptor protein 1	protein	286	69% helix, 1% strand	Q96A54
H	The heavy chain variable domain (antibody)	protein	119	8% helix, 49% strand	—
L	The light chain variable domain (antibody)	protein	107	3% helix, 51% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · chains A
PO4 · Phosphate ion · ion · chains A, L

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	505	0.84	0.90	65	empty
2	199	0.52	0.77	40	empty
3	63	0.33	0.77	18	empty
4	75	0.30	0.74	25	empty

Interfaces

3 interfaces between chains.

H–L · 820 Å² buried · 7 hydrogen bonds · protein-protein
A–L · 522 Å² buried · 7 hydrogen bonds · protein-protein
A–H · 445 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6KS0 · Crystal structure of the human adiponectin receptor 1 · the same entry in another collection · chain A against A, TM-score 1.00
Q96A54 · AlphaFold monomer V2.0 prediction for adiponectin receptor protein 1 (Q96A54) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q96A54
Elsewhere: RCSB PDB 6KS0 · PDBe 6KS0 · UniProt Q96A54

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