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2k01

Structure of a locked SDF1 dimer

Method: SOLUTION NMR Dmax: 50.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Stromal cell-derived factor 1

Homo sapiens

UniProt P48061

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 22–89 Chain C； UniProt 22–89 Fragment：SDF-1-alpha(3-67) domain Mutation：L36C,A65C No other associated polymer 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

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2K01 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A15 SDF-1ALPHA Deposited 1997-12-22 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
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 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
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 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
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 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
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 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
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
2K03 Structure of SDF1 in complex with the CXCR4 N-terminus containing a sulfotyrosine at postition 21 Deposited 2008-01-24 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
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 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
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 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
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 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
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 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
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 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
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 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
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 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
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 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
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 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
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 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
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 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
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 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
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 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
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 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
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 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
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 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
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 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
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 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
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

31 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SDF1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–70； UniProt 22–89 Author chain C； PDBConstruct 3–70； UniProt 22–89

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2k01

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2k01
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2k01
Deposition date deposition_date2008-01-23
Structure title titleStructure of a locked SDF1 dimer
Keywords keywords;stromal cell derived factor-1, SDF1-alpha, CXCL12, chemokine, sulfotyrosine, locked dimer, Alternative splicing, Chemotaxis, Cytokine, Growth factor, Secreted ;; CYTOKINE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.91 Å
Radius of gyration Rg (electron density) rg_electron14.53 Å
Forward intensity I(0) i01404280000.00
Molecular weight molecular_weight319440.0 kDa
Excluded volume excluded_volume401700 ų
Envelope volume envelope_volume38683 ų
Hydration-shell volume shell_volume18646 ų
Envelope diameter envelope_diameter55.6 Å
Shell Rg shell_rg23.57 Å
Envelope Rg envelope_rg17.13 Å
Shape Rg shape_rg14.54 Å
Total Rg total_rg14.62 Å
Total atoms total_atoms45460
Residues n_residues2720
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax50.2 Å
Rg (real space) rg_real14.79 Å
Rg uncertainty (real space) rg_real_error0.39 Å
I(0) (real space) i0_real1.4040e+09
I(0) uncertainty (real space) i0_real_error1.6530e+07
Rg (reciprocal space) rg_reciprocal14.80 Å
I(0) (reciprocal space) i0_reciprocal1404000000.0000
Solution quality estimate total_estimate0.8638
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.3 Å
Skewness Skewness skewness0.021
Kurtosis Kurtosis kurtosis-0.472
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha703600.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.746; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.997
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2k01a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.9 — IL8-like
Superfamily Superfamily superfamilyd.9.1 — Interleukin 8-like chemokines
Family Family familyd.9.1.1 — Interleukin 8-like chemokines
Domain ID domain_idd2k01c_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.9 — IL8-like
Superfamily Superfamily superfamilyd.9.1 — Interleukin 8-like chemokines
Family Family familyd.9.1.1 — Interleukin 8-like chemokines

CATH v4.4 (2 domains)

Domain ID domain_id2k01A00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily40 —
Domain ID domain_id2k01C00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily40 —
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8. Citations (1)

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9. Files and Curves (10)