Macromolecule Content

Total Structure Weight: 82.17 kDa
Atom Count: 5222
Modelled Residue Count: 637
Deposited Residue Count: 680
Unique protein chains: 1

3HP3

Crystal structure of CXCL12

DOI: 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.

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

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: 10.1002/prot.22666
Primary Citation of Related Structures:
3GV3, 3HP3

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CXCL12 protein	A, B, C, D, E, F, G, H,	A, B, C, D, E, F, G, H, I, J	68	Homo sapiens	Mutation(s): 0 Gene Names: CXCL12, hCG_25667, SDF1, SDF1A, SDF1B
Find proteins for P48061 (Homo sapiens) Explore P48061 Go to UniProtKB: P48061
NIH Common Fund Data Resources
PHAROS: P48061 GTEx: ENSG00000107562
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AU Query on AU Download Ideal Coordinates CCD File SDF format, chain K [A] SDF format, chain L [A] SDF format, chain M [B] SDF format, chain N [C] SDF format, chain O [D] SDF format, chain P [E] SDF format, chain Q [E] SDF format, chain R [G] SDF format, chain S [H] SDF format, chain T [H] SDF format, chain U [I] SDF format, chain V [J] MOL2 format, chain K [A] MOL2 format, chain L [A] MOL2 format, chain M [B] MOL2 format, chain N [C] MOL2 format, chain O [D] MOL2 format, chain P [E] MOL2 format, chain Q [E] MOL2 format, chain R [G] MOL2 format, chain S [H] MOL2 format, chain T [H] MOL2 format, chain U [I] MOL2 format, chain V [J]	A, B, C, D, E, G, H, I, J	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N		Ligand Interaction

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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2009-06-03
Released Date: 2010-01-26

Deposition Author(s):

Revision History (Full details and data files)

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

Prepare Data

Validate Data

Deposit Data

Deposition Help & Resources

176773 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

3HP3

Crystal structure of CXCL12

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

Entity ID: 1

NIH Common Fund Data Resources

Protein Feature View

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)