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.

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

Organizational Affiliation

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CXCL12 protein	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48061
Sequence Annotations 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 [auth A] SDF format, chain L [auth A] SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain P [auth E] SDF format, chain Q [auth E] SDF format, chain R [auth G] SDF format, chain S [auth H] SDF format, chain T [auth H] SDF format, chain U [auth I] SDF format, chain V [auth J] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth G] MOL2 format, chain S [auth H] MOL2 format, chain T [auth H] MOL2 format, chain U [auth I] MOL2 format, chain V [auth J]	K [auth A] L [auth A] M [auth B] N [auth C] O [auth D] 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		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth G] Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth G] Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth J]

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

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

Help and Resources

3HP3

Crystal structure of CXCL12

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)