2NWG

Structure of CXCL12:heparin disaccharide complex

• PDB DOI: https://doi.org/10.2210/pdb2NWG/pdb

• Classification: CYTOKINE,SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-11-14 Released: 2007-02-13 
• Deposition Author(s): Murphy, J.W., Cho, Y., Lolis, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.265 
• R-Value Work: 0.240 
• R-Value Observed: 0.241 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 17.14 kDa 
• Atom Count: 1,207 
• Modelled Residue Count: 132 
• Deposited Residue Count: 136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stromal cell-derived factor 1	A, B	68	Homo sapiens	Mutation(s): 0  Gene Names: CXCL12, SDF1
UniProt & NIH Common Fund Data Resources
Find proteins for P48061 (Homo sapiens) Explore P48061  Go to UniProtKB:  P48061
PHAROS:  P48061 GTEx:  ENSG00000107562

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G01871HO GlyCosmos:  G01871HO

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900026	C, D	HEPARIN DISACCHARIDE I-S,	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.265 
• R-Value Work: 0.240 
• R-Value Observed: 0.241 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.492	α = 90
b = 56.965	β = 90
c = 71.747	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-13 
Deposition Author(s): Murphy, J.W., Cho, Y., Lolis, E.

Revision History  

• Version 1.0: 2007-02-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-12-27
  Changes: Data collection, Database references, Structure summary