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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P48061 New Search
32PDB entries
33Biological assembly
56chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
1A15 SDF-1ALPHA Deposited 1997-12-22 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 22–88（67 aa）
Chain B 22–88（67 aa）
Mutation：N33A Mutation：N33A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；PROTEIN CONCENTRATION 10MG/ML. WELL SOLUTION 1.9M AMMONIUM SULFATE 0.1M TRIS-HCL PH 8.5. CRYSTALLIZED USING VAPOR DIFFUSION., vapor diffusion
Resolution 2.20 Å R-free 0.298
1QG7 STROMA CELL-DERIVED FACTOR-1ALPHA (SDF-1ALPHA) Deposited 1999-04-21 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 22–88（67 aa）
Chain B 22–88（67 aa）
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.0
Resolution 2.00 Å R-free 0.258
1SDF SOLUTION STRUCTURE OF STROMAL CELL-DERIVED FACTOR-1 (SDF-1), NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-11-15 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 22–88（67 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.9；303 K
Resolution not provided
1VMC STROMA CELL-DERIVED FACTOR-1ALPHA (SDF-1ALPHA) Deposited 2004-09-20 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 22–89（68 aa） Fragment：SDF-1ALPHA (residues 22-89)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；308 K；Ionic strength (raw mmCIF value) 50 mM SODIUM PHOSPHATE
Resolution not provided
2J7Z Crystal Structure of recombinant Human Stromal Cell-Derived Factor- 1alpha Deposited 2006-10-18 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 22–89（68 aa） Fragment：RESIDUES 22-89
Chain B 22–89（68 aa） Fragment：RESIDUES 22-89
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.95 Å R-free 0.247
2K01 Structure of a locked SDF1 dimer Deposited 2008-01-23 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 22–89（68 aa） Fragment：SDF-1-alpha(3-67) domain
Chain C 22–89（68 aa） Fragment：SDF-1-alpha(3-67) domain
Mutation：L36C,A65C Mutation：L36C,A65C No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 21；Pressure AMBIENT
NMR sample composition 0.620 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2K03 Structure of SDF1 in complex with the CXCR4 N-terminus containing a sulfotyrosine at postition 21 Deposited 2008-01-24 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 22–89（68 aa） Fragment：SDF-1-alpha(3-67) domain
Chain C 22–89（68 aa） Fragment：SDF-1-alpha(3-67) domain
Mutation：L36C,A65C Mutation：L36C,A65C No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；308 K；Ionic strength (raw mmCIF value) 21；Pressure AMBIENT
NMR sample composition .338 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, .970 mM CXCR4, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1.07 mM [U-100% 13C; U-100% 15N] CXCR4, 0.67 mM CXCL12/SDF1-alpha, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2K04 Structure of SDF1 in complex with the CXCR4 N-terminus containing no sulfotyrosines Deposited 2008-01-24 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 22–89（68 aa） Fragment：SDF-1-alpha(3-67) domain
Chain C 22–89（68 aa） Fragment：SDF-1-alpha(3-67) domain
Mutation：L36C,A65C Mutation：L36C,A65C No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；308 K；Ionic strength (raw mmCIF value) 21；Pressure AMBIENT
NMR sample composition .31 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, .775 mM CXCR4, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.0 mM [U-100% 13C; U-100% 15N] CXCR4, 0.625 mM CXCL12/SDF1-alpha, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2K05 Structure of SDF1 in complex with the CXCR4 N-terminus containing sulfotyrosines at postitions 7, 12 and 21 Deposited 2008-01-24 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain A 22–89（68 aa） Fragment：SDF-1-alpha(3-67) domain
Chain C 22–89（68 aa） Fragment：SDF-1-alpha(3-67) domain
Mutation：L36C,A65C Mutation：L36C,A65C No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；308 K；Ionic strength (raw mmCIF value) 21；Pressure AMBIENT
NMR sample composition .338 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, .97 mM CXCR4, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1.07 mM [U-100% 13C; U-100% 15N] CXCR4, 0.67 mM CXCL12/SDF1-alpha, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2KEC Structure of SDF-1/CXCL12 Deposited 2009-01-28 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 22–89（68 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure AMBIENT
NMR sample composition 1.56 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2KED Structure of SDF-1/CXCL12 Deposited 2009-01-28 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 22–89（68 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 0.001；Pressure AMBIENT
NMR sample composition 1.6 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2KEE Structure of SDF-1/CXCL12 Deposited 2009-01-28 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 22–89（68 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.001 mM；Pressure AMBIENT
NMR sample composition 1.2 mM CXCL12/SDF1-alpha, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2KOL Solution structure of human SDF1-alpha H25R Deposited 2009-09-24 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 22–89（68 aa） Fragment：SDF-1-alpha, residues 22-89
Mutation：H25R No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 20；Pressure AMBIENT
NMR sample composition 3.3 mM [U-100% 13C; U-100% 15N] SDF1a H25R, 25 mM [U-99% 2H] MES, 0.02 % sodium azide, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2N55 Structure of constitutively monomeric CXCL12 in complex with the CXCR4 N-terminus Deposited 2015-07-07 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 22–89（68 aa）
Mutation：L76C, I79C No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient
NMR sample composition 2 mM [U-99% 13C; U-99% 15N] protein_1, 25 mM [U-2H] MES, 10 % [U-99% 2H] D2O, 0.02 % sodium azide, 2 mM protein_2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-99% 13C; U-99% 15N] protein_2, 25 mM [U-2H] MES, 0.02 % sodium azide, 10 % [U-99% 2H] D2O, 2 mM protein_1, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2NWG Structure of CXCL12:heparin disaccharide complex Deposited 2006-11-14 Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 22–88（67 aa） Fragment：residues 22-88
Chain B 22–88（67 aa） Fragment：residues 22-88
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions Soaking；pH 8.5；298 K；Grown in 2M Ammonium Sulfate, 0.1M TrisHCl pH 8.50. Soaked in 20 mM PEG-8000, 1M TrisHCl pH 8.5, 16 mM disaccharide. , Soaking, temperature 298K
Resolution 2.07 Å R-free 0.265
2SDF SOLUTION NMR STRUCTURE OF STROMAL CELL-DERIVED FACTOR-1 (SDF-1), 30 STRUCTURES Deposited 1998-03-07 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 22–88（67 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.9；303 K
Resolution not provided
4LMQ Development and Preclinical Characterization of a Humanized Antibody Targeting CXCL12 Deposited 2013-07-10 Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain D 29–89（61 aa） Fragment：UNP RESIDUES 29-89
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；0.2M NaF, 0.1M Bis-tris, propane, 23%w/v PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.77 Å R-free 0.301
4LMQ Development and Preclinical Characterization of a Humanized Antibody Targeting CXCL12 Deposited 2013-07-10 Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count
Chain F 29–89（61 aa） Fragment：UNP RESIDUES 29-89
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；0.2M NaF, 0.1M Bis-tris, propane, 23%w/v PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.77 Å R-free 0.301
4UAI Crystal structure of CXCL12 in complex with inhibitor Deposited 2014-08-09 Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 22–89（68 aa） Fragment：UNP residues 22-89
Chain B 22–89（68 aa） Fragment：UNP residues 22-89
Not recorded 3GG 1-phenyl-3-[4-(1H-tetrazol-5-yl)phenyl]urea × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；2 M AmSO4, 2% MPD, 0.1 M MES Sodium Salt pH 6.5
Resolution 1.90 Å R-free 0.235
6SHR X-RAY CRYSTAL STRUCTURE OF CELL-FREE PROTEIN SYNTHESIS (CFPS) PRODUCED SDF1-A Deposited 2019-08-08 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 26–89（64 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M tri-sodium citrate pH 5.6, 20 % (v/v) isopropanol and 20 % (w/v) PEG 4000
Resolution 1.75 Å R-free 0.239
7SK3 Cryo-EM structure of ACKR3 in complex with CXCL12, an intracellular Fab, and an extracellular Fab Deposited 2021-10-19 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain B 22–89（68 aa） Fragment：UNP residues 22-89
Not recorded CLR CHOLESTEROL × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7SK4 Cryo-EM structure of ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ, an intracellular Fab, and an extracellular Fab Deposited 2021-10-19 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain B 22–89（68 aa）
Mutation：N-terminus of CXCL12 (KPV) substituted with LRHQ CLR CHOLESTEROL × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7SK5 Cryo-EM structure of ACKR3 in complex with CXCL12 and an intracellular Fab Deposited 2021-10-19 Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
Chain B 22–89（68 aa） Fragment：UNP residues 22-89
Not recorded CLR CHOLESTEROL × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7SK6 Cryo-EM structure of human ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ and an intracellular Fab Deposited 2021-10-19 Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count
Chain B 22–89（68 aa）
Mutation：N-terminus of CXCL12 (KPV) substituted with LRHQ No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7SK7 Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial agonist CCX662, and an extracellular Fab Deposited 2021-10-19 Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
Chain B 22–89（68 aa） Fragment：UNP residues 22-89
Not recorded GJ9 (1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium × 1 CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7SK8 Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial agonist CCX662, an extracellular Fab, and an intracellular Fab Deposited 2021-10-19 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain B 22–89（68 aa） Fragment：UNP residues 22-89
Not recorded CLR CHOLESTEROL × 6 LMN Lauryl Maltose Neopentyl Glycol × 1 GJ9 (1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1-yl)-1,3-thiazol-4-yl]methyl}-1,4-diazepan-1-ium × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8K3Z Cryo-EM structure of CXCR4 in complex with CXCL12 Deposited 2023-07-17 Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain D 22–83（62 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å
8U4O Structure of CXCL12-bound CXCR4/Gi complex Deposited 2023-09-11 Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
Chain J 22–89（68 aa） Fragment：UNP residues 22-89
Not recorded CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.29 Å
9E82 ACKR3 phosphorylated by GRK5 in complex with arrestin2 and Fab7 Deposited 2024-11-04 Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count
Chain B 25–89（65 aa）
Not recorded CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9ME1 hCXCR4-CXCL12 complex with 1:1 stoichiometry Deposited 2024-12-05 Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein count
Chain F 22–93（72 aa）
Chain G 22–93（72 aa）
Chain H 22–93（72 aa）
Chain J 22–93（72 aa）
Chain M 22–93（72 aa）
Chain N 22–93（72 aa）
Chain O 22–93（72 aa）
Chain P 22–93（72 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
9MEU CXCR4 tetramer bound to 4 CXCL12 dimers Deposited 2024-12-08 Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric（12） Consistent with protein count
Chain F 22–93（72 aa）
Chain G 22–93（72 aa）
Chain H 22–93（72 aa）
Chain J 22–93（72 aa）
Chain M 22–93（72 aa）
Chain N 22–93（72 aa）
Chain O 22–93（72 aa）
Chain P 22–93（72 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9UPU Cryo-EM strucutre of CXCR4 complexed with agonist SDV1a Deposited 2025-04-29 Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain J 22–29（8 aa） Fragment：N-terminus
Not recorded CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9UPV Cryo-EM structure of CXCR4 complexed with agonist SDVX1 Deposited 2025-04-29 Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count
Chain J 22–29（8 aa） Fragment：N-terminus
Not recorded CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.