5E4L

Structure of ligand binding region of uPARAP at pH 5.3

• PDB DOI: https://doi.org/10.2210/pdb5E4L/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): Yes 


• Deposited: 2015-10-06 Released: 2016-10-12 
• Deposition Author(s): Yuan, C., Huang, M.
• Funding Organization(s): Natural Science Foundation Of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.259 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 

Literature

Crystal structures of uPARAP, a member of mannose receptor family

Yuan, C., Huang, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 112.45 kDa 
• Atom Count: 6,747 
• Modelled Residue Count: 814 
• Deposited Residue Count: 984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-type mannose receptor 2	A, B	492	Homo sapiens	Mutation(s): 1  Gene Names: MRC2, CLEC13E, ENDO180, KIAA0709, UPARAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBG0 (Homo sapiens) Explore Q9UBG0  Go to UniProtKB:  Q9UBG0
PHAROS:  Q9UBG0 GTEx:  ENSG00000011028

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.259 
• R-Value Work: 0.217 
• R-Value Observed: 0.219 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.27	α = 90
b = 102.7	β = 94.54
c = 87.76	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-10-12 
Deposition Author(s): Yuan, C., Huang, M.

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Funding Organization	Location	Grant Number
Natural Science Foundation Of China	China	31570745

Revision History  

• Version 1.0: 2016-10-12
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary