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Human oxidized low density lipoprotein receptor lox-1 P3 1 21 space group

Analyse Human oxidized low density lipoprotein receptor lox-1 P3 1 21 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YPO
Type: protein
Length: 1,043 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oxidised low density lipoprotein (lectin-like) receptor 1
UniProt: P78380
Pockets: 11 · best druggability 0.65

Structure

x-ray diffraction · 4 distinct chains · 15% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Oxidised low density lipoprotein (lectin-like) receptor 1	protein	130	15% helix, 33% strand	P78380
B, C, G	Oxidised low density lipoprotein (lectin-like) receptor 1	protein	132	16% helix, 33% strand	P78380
D, E, H	Oxidised low density lipoprotein (lectin-like) receptor 1	protein	129	14% helix, 33% strand	P78380
F	Oxidised low density lipoprotein (lectin-like) receptor 1	protein	130	16% helix, 32% strand	P78380

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	369	0.65	0.80	32	empty
2	288	0.65	0.82	29	empty
3	314	0.65	0.81	32	empty
4	152	0.60	0.83	30	empty
5	335	0.59	0.77	61	empty

Interfaces

8 interfaces between chains.

C–D · 1007 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 944 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 913 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 910 Å² buried · 10 hydrogen bonds · protein-protein
A–E · 484 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

1YPO · Human Oxidized Low Density Lipoprotein Receptor LOX-1 P3 1 21 Space Group · the same entry in another collection · chain H against H, TM-score 1.00
P78380 · AlphaFold monomer V2.0 prediction for oxidized low-density lipoprotein receptor 1 (P78380) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P78380
Elsewhere: RCSB PDB 1YPO · PDBe 1YPO · UniProt P78380

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