Macromolecule Content

Total Structure Weight: 9.70 kDa
Atom Count: 668
Modelled Residue Count: 79
Deposited Residue Count: 85
Unique protein chains: 1

5B4Y

Crystal structure of the LA12 fragment of ApoER2

PDB DOI: 10.2210/pdb5B4Y/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-04-20 Released: 2017-04-26
Deposition Author(s): Nogi, T., Tabata, S., Hirai, H., Yasui, N., Takagi, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.247
R-Value Work: 0.210
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the ectodomain from a LDLR close homologue in complex with its physiological ligand.

Hirai, H., Yasui, N., Yamashita, K., Tabata, S., Yamamoto, M., Takagi, J., Nogi, T.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low-density lipoprotein receptor-related protein 8	A [auth B]	85	Homo sapiens	Mutation(s): 0 Gene Names: LRP8, APOER2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14114 (Homo sapiens) Explore Q14114 Go to UniProtKB: Q14114
PHAROS: Q14114 GTEx: ENSG00000157193
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q14114
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B SDF format, chain C [auth B] MOL2 format, chain B MOL2 format, chain C [auth B]	B, C [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.247
R-Value Work: 0.210
R-Value Observed: 0.212
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.162	α = 90
b = 41.78	β = 90
c = 55.063	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2016-04-20
Released Date: 2017-04-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-04-26
Type: Initial release
Version 1.1: 2020-02-26
Changes: Data collection

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.