2ZG1

Crystal Structure of Two N-terminal Domains of Siglec-5 in Complex with 6'-Sialyllactose

• PDB DOI: https://doi.org/10.2210/pdb2ZG1/pdb

• Classification: IMMUNE SYSTEM/CARBOHYDRATE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-01-17 Released: 2008-02-05 
• Deposition Author(s): Zhuravleva, M.A., Sun, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.275 
• R-Value Work: 0.246 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 24.64 kDa 
• Atom Count: 1,729 
• Modelled Residue Count: 208 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sialic acid-binding Ig-like lectin 5	A	214	Homo sapiens	Mutation(s): 0  Gene Names: SIGLEC5
UniProt & NIH Common Fund Data Resources
Find proteins for O15389 (Homo sapiens) Explore O15389  Go to UniProtKB:  O15389
PHAROS:  O15389

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIA	B [auth A]	N-acetyl-alpha-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-YRMXFSIDSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SIA	PDBBind:  2ZG1	Kd: 8.00e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.275 
• R-Value Work: 0.246 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.044	α = 90
b = 94.044	β = 90
c = 209.888	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-05 
Deposition Author(s): Zhuravleva, M.A., Sun, P.D.

Revision History  

• Version 1.0: 2008-02-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-11-01
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary