2NWG: CXCL12:heparin disaccharide complex

Structure of CXCL12:heparin disaccharide complex. Determined by X-ray diffraction at 2.07 Å resolution. Released 13 Feb 2007.

Method: X-ray diffraction
Resolution: 2.07 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,207
Mol. weight: 17.14 kDa
Released: 13 Feb 2007

Explore 2NWG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2NWG contains 4 α-helices and 10 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	1
α-helix	20-22	3
β-strand	23-29	7	2
β-strand	38-42	5	2
β-strand	48-50	3	2
β-strand	51	1	1
α-helix	58-66	9

Chain B: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	3
α-helix	20-22	3
β-strand	23-29	7	2
β-strand	38-42	5	2
β-strand	48-50	3	2
β-strand	51	1	3
α-helix	56-66	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Stromal cell-derived factor 1	A, B	protein	68	Homo sapiens	P48061 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2NWG_1 Stromal cell-derived factor 1 (chains A, B)
MKPVSLSYRCPCRFFESHIARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQ
EYLEKALN

Primary citation

Structural and Functional Basis of CXCL12 (Stromal Cell-derived Factor-1{alpha}) Binding to Heparin. Murphy, J.W., Cho, Y., Sachpatzidis, A. et al. J Biol Chem (2007) 282:10018-10027. DOI 10.1074/jbc.M608796200 · PubMed

Other PDB entries of the same protein (UniProt P48061 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3GV3 1.6 Å, CXCL12 (SDF) in trigonal space group
6SHR 1.75 Å, X-ray crystal structure of cell-free protein synthesis (CFPS) produced SDF1-a
4UAI 1.9 Å, Crystal structure of CXCL12 in complex with inhibitor
2J7Z 1.95 Å, Crystal Structure of recombinant Human Stromal Cell-Derived Factor- 1alpha
1QG7 2.0 Å, Stroma cell-derived factor-1ALPHA (sdf-1ALPHA)
1A15 2.2 Å, Sdf-1ALPHA
3HP3 2.2 Å, Crystal structure of CXCL12
9UPV 2.7 Å, Cryo-EM structure of CXCR4 complexed with agonist SDVX1
4LMQ 2.77 Å, Development and Preclinical Characterization of a Humanized Antibody Targeting CXCL12
9UPU 2.8 Å, Cryo-EM strucutre of CXCR4 complexed with agonist SDV1a
8K3Z 2.81 Å, Cryo-EM structure of CXCR4 in complex with CXCL12
8U4O 3.29 Å, Structure of CXCL12-bound CXCR4/Gi complex

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