1SL5

Crystal Structure of DC-SIGN carbohydrate recognition domain complexed with LNFP III (Dextra L504).

• PDB DOI: https://doi.org/10.2210/pdb1SL5/pdb

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


• Deposited: 2004-03-05 Released: 2004-06-15 
• Deposition Author(s): Guo, Y., Feinberg, H., Conroy, E., Mitchell, D.A., Alvarez, R., Blixt, O., Taylor, M.E., Weis, W.I., Drickamer, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.223 
• R-Value Work: 0.179 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.93 kDa 
• Atom Count: 1,325 
• Modelled Residue Count: 131 
• Deposited Residue Count: 139 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mDC-SIGN1B type I isoform	A	139	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NNX6 (Homo sapiens) Explore Q9NNX6  Go to UniProtKB:  Q9NNX6
PHAROS:  Q9NNX6 GTEx:  ENSG00000090659

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose	B	4		N/A
Glycosylation Resources
GlyTouCan:  G81345OW GlyCosmos:  G81345OW GlyGen:  G81345OW

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.223 
• R-Value Work: 0.179 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.57	α = 90
b = 55.37	β = 90
c = 29.63	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-15 
Deposition Author(s): Guo, Y., Feinberg, H., Conroy, E., Mitchell, D.A., Alvarez, R., Blixt, O., Taylor, M.E., Weis, W.I., Drickamer, K.

Revision History  

• Version 1.0: 2004-06-15
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary