6TL7 | pdb_00006tl7

CRYSTAL STRUCTURE OF LECTIN-LIKE OX-LDL RECEPTOR 1 (P212121)

• PDB DOI: https://doi.org/10.2210/pdb6TL7/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: 1.11 Å
• R-Value Free: 
  0.162 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

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 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 30.88 kDa 
• Atom Count: 2,887 
• Modeled Residue Count: 268 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidized low-density lipoprotein receptor 1	A, B	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	C [auth A], D [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.11 Å
• R-Value Free:  0.162 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.49	α = 90
b = 64.7	β = 90
c = 101.85	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
BUSTER-TNT	refinement
SCALA	data scaling
Coot	model building
autoPROC	data processing
XDS	data processing
autoPROC	data reduction

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, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary