7R8U | pdb_00007r8u

LOX-1 - Structural and Functional Studies of a Receptor Implicated in Atherosclerosis

• PDB DOI: https://doi.org/10.2210/pdb7R8U/pdb

• Classification: SIGNALING PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2021-06-27 Released: 2022-06-01 
• Deposition Author(s): Oganesyan, V., van Dyk, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.218 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.194 (DCC) 

Starting Model: experimental

Literature

Structural and functional studies of a monoclonal antibody blocking LOX-1

Ongstad, E.L., Gaddipati, R., Belkhodja, M., van Dyk, N., Levy, S., Sagar, D., Cariuk, P., Wolny, M., Hanna, R.N., Borrok, M.J., Buchanan, A., Oganesyan, V., Gupta, R.

(2023) Commun Med 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 77.98 kDa 
• Atom Count: 6,010 
• Modeled Residue Count: 704 
• Deposited Residue Count: 710 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidized low-density lipoprotein receptor 1	A [auth AAA], B [auth BBB]	132	Homo sapiens	Mutation(s): 0  Gene Names: OLR1, CLEC8A, LOX1
UniProt & NIH Common Fund Data Resources
Find proteins for P78380 (Homo sapiens) Explore P78380  Go to UniProtKB:  P78380
PHAROS:  P78380 GTEx:  ENSG00000173391

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen binding fragment, Vh and Ch1	C [auth HHH]	230	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody light chain, kappa	D [auth LLL]	216	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth AAA], F [auth BBB], G [auth BBB], H [auth LLL], I [auth LLL]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.218 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.194 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.908	α = 90
b = 89.901	β = 90
c = 110.925	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-06-01 
Deposition Author(s): Oganesyan, V., van Dyk, N.

Revision History  

• Version 1.0: 2022-06-01
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-29
  Changes: Database references
• Version 1.3: 2024-10-23
  Changes: Structure summary