4N36

Structure of langerin CRD I313 D288 complexed with Me-GlcNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-type lectin domain family 4 member K
A, B, C, D
136Homo sapiensMutation(s): 3 
Gene Names: CD207CLEC4K
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJ71 (Homo sapiens)
Explore Q9UJ71 
Go to UniProtKB:  Q9UJ71
PHAROS:  Q9UJ71
GTEx:  ENSG00000116031 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UJ71
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2F8
Query on 2F8

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
methyl 2-acetamido-2-deoxy-alpha-D-glucopyranoside
C9 H17 N O6
ZEVOCXOZYFLVKN-OKNNCHMLSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
M [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.55α = 90
b = 79.55β = 90
c = 89.88γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2013-12-04
    Changes: Database references
  • Version 1.2: 2014-01-22
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.5: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary