3HP3

Crystal structure of CXCL12

• PDB DOI: https://doi.org/10.2210/pdb3HP3/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-03 Released: 2010-01-26 
• Deposition Author(s): Murphy, J.W., Lolis, E., Xiong, Y., Yuan, H., Crichlow, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.280 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 

Literature

Heterologous quaternary structure of CXCL12 and its relationship to the CC chemokine family

Murphy, J.W., Yuan, H., Kong, Y., Xiong, Y., Lolis, E.J.

(2009) Proteins 78: 1331-1337

• PubMed: 20077567 
• DOI: https://doi.org/10.1002/prot.22666
• Primary Citation of Related Structures:  
  3GV3, 3HP3

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Organizational Affiliation: 

Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.

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)

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82.17 kDa 
• Atom Count: 5,222 
• Modelled Residue Count: 637 
• Deposited Residue Count: 680 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CXCL12 protein	A, B, C, D, E, F, G, H, I, J	68	Homo sapiens	Mutation(s): 0  Gene Names: CXCL12, hCG_25667
UniProt & NIH Common Fund Data Resources
Find proteins for P48061 (Homo sapiens) Explore P48061  Go to UniProtKB:  P48061
PHAROS:  P48061 GTEx:  ENSG00000107562

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AU	K [auth A], L [auth A], M [auth B], N [auth C], O [auth D], P [auth E], Q [auth E], R [auth G], S [auth H], T [auth H], U [auth I], V [auth J]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.280 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.834	α = 90
b = 117.468	β = 90
c = 134.501	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-26 
Deposition Author(s): Murphy, J.W., Lolis, E., Xiong, Y., Yuan, H., Crichlow, G.

Revision History  

• Version 1.0: 2010-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2018-05-30
  Changes: Advisory, Data collection, Derived calculations
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary