Research workbench

Revised crystal structure of the human adiponectin receptor 1 in an open conformation

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

PDB: 5LXG
Type: protein
Length: 508 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adiponectin receptor protein 1; V region heavy chain; V region light chain
UniProt: Q96A54
Ligands: ZN, SO4
Pockets: 5 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adiponectin receptor protein 1	protein	282	67% helix, 1% strand	Q96A54
H	V region heavy chain	protein	119	8% helix, 52% strand	—
L	V region light chain	protein	107	3% helix, 51% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A, L

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	848	0.79	0.82	74	empty
2	153	0.47	0.77	33	empty
3	58	0.37	0.79	17	empty
4	63	0.31	0.75	17	empty
5	56	0.27	0.74	18	empty

Interfaces

3 interfaces between chains.

H–L · 797 Å² buried · 9 hydrogen bonds · protein-protein
A–L · 510 Å² buried · 5 hydrogen bonds · protein-protein
A–H · 442 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5LXG · Revised crystal structure of the human adiponectin receptor 1 in an open conformation · 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 0.93

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 5LXG · PDBe 5LXG · UniProt Q96A54

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