6TL9

CRYSTAL STRUCTURE OF LECTIN-LIKE OX-LDL RECEPTOR 1 IN COMPLEX WITH BI-0115

• PDB DOI: https://doi.org/10.2210/pdb6TL9/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-02 Released: 2020-07-22 
• Deposition Author(s): Nar, H., Fiegen, D., Schnapp, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free: 0.246 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 

Starting Model: experimental

Literature

A small-molecule inhibitor of lectin-like oxidized LDL receptor-1 acts by stabilizing an inactive receptor tetramer state

Nar, H., Fiegen, D., Schnapp, G.

(2020) Commun Chem 

• DOI: https://doi.org/10.1038/s42004-020-0321-2

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 124.28 kDa 
• Atom Count: 8,628 
• Modelled Residue Count: 1,038 
• Deposited Residue Count: 1,080 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidized low-density lipoprotein receptor 1	A, B, C, D, E, F, G, H	135	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NJT (Subject of Investigation/LOI)	J [auth B], K [auth B], L [auth F], M [auth F]	9-chloranyl-5-propyl-11~{H}-pyrido[2,3-b][1,4]benzodiazepin-6-one C15 H14 Cl N3 O QTCZUCSALXBZQR-UHFFFAOYSA-N
GOL	I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free: 0.246 
• R-Value Work: 0.222 
• R-Value Observed: 0.223 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.816	α = 90
b = 62.211	β = 93.99
c = 116.331	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
XDS	data reduction
autoPROC	data scaling
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-22 
Deposition Author(s): Nar, H., Fiegen, D., Schnapp, G.

Revision History  

• Version 1.0: 2020-07-22
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary