4UAI: CXCL12

Crystal structure of CXCL12 in complex with inhibitor. Determined by X-ray diffraction at 1.9 Å resolution. Released 12 Nov 2014.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,178
Mol. weight: 16.43 kDa
Ligands: 3GG
Released: 12 Nov 2014

Explore 4UAI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4UAI contains 6 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: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
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: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
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

>4UAI_1 Stromal cell-derived factor 1 (chains A, B)
KPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQE
YLEKALNK

Ligands and cofactors

ID	Name	Formula	Copies
3GG	1-phenyl-3-[4-(1H-tetrazol-5-yl)phenyl]urea	C14 H12 N6 O	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural Analysis of a Novel Small Molecule Ligand Bound to the CXCL12 Chemokine. Smith, E.W., Liu, Y., Getschman, A.E. et al. J Med Chem (2014) 57:9693-9699. DOI 10.1021/jm501194p · 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
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)
2NWG 2.07 Å, Structure of CXCL12:heparin disaccharide complex
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

Browse structure collections

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