SAXSdb — 1don

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1. Protein Identity and Related Structures Protein Identity & Related Structures

MCP-1

Homo sapiens

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 24–99 Chain B； UniProt 24–99	Not recorded	No other associated polymer	SOLUTION NMR mmCIF provides none of the parsed experimental conditions	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 1DON	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DOK MONOCYTE CHEMOATTRACTANT PROTEIN 1, P-FORM Deposited 1996-11-27	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 24–99（76 aa） Chain B 24–99（76 aa）	Mutation：N-TERMINAL METHIONINE NOT REMOVED POST-TRANSLATIONALLY Mutation：N-TERMINAL METHIONINE NOT REMOVED POST-TRANSLATIONALLY	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；10 MG/ML PROTEIN IN 50 MM TRIS BUFFER PH 7.5-8 EQUILIBRATED AGAINST 50-55% AMMONIUM SULFATE USING HANGING DROP VAPOR DIFFUSION METHOD., pH 8.0, vapor diffusion - hanging drop	Resolution 1.85 Å R-free 0.245
1DOK MONOCYTE CHEMOATTRACTANT PROTEIN 1, P-FORM Deposited 1996-11-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–99（76 aa） Chain B 24–99（76 aa）	Mutation：N-TERMINAL METHIONINE NOT REMOVED POST-TRANSLATIONALLY Mutation：N-TERMINAL METHIONINE NOT REMOVED POST-TRANSLATIONALLY	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；10 MG/ML PROTEIN IN 50 MM TRIS BUFFER PH 7.5-8 EQUILIBRATED AGAINST 50-55% AMMONIUM SULFATE USING HANGING DROP VAPOR DIFFUSION METHOD., pH 8.0, vapor diffusion - hanging drop	Resolution 1.85 Å R-free 0.245
1DOL MONOCYTE CHEMOATTRACTANT PROTEIN 1, I-FORM Deposited 1996-11-22	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 24–99（76 aa）	Mutation：INS(MET0)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；10 MG/ML PROTEIN IN 50 MM TRIS BUFFER PH 7.5-8 EQUILIBRATED AGAINST 50-55% AMMONIUM SULFATE USING HANGING DROP VAPOR DIFFUSION METHOD., pH 8.0, vapor diffusion - hanging drop	Resolution 2.40 Å R-free 0.275
1DOL MONOCYTE CHEMOATTRACTANT PROTEIN 1, I-FORM Deposited 1996-11-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–99（76 aa）	Mutation：INS(MET0)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；10 MG/ML PROTEIN IN 50 MM TRIS BUFFER PH 7.5-8 EQUILIBRATED AGAINST 50-55% AMMONIUM SULFATE USING HANGING DROP VAPOR DIFFUSION METHOD., pH 8.0, vapor diffusion - hanging drop	Resolution 2.40 Å R-free 0.275
1DOM SOLUTION STRUCTURE OF THE MONOCYTE CHEMOATTRACTANT PROTEIN-1 DIMER USING HETERONUCLEAR, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-01-21	Parsed fields agree	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 24–99（76 aa） Chain B 24–99（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1ML0 VIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS68 IN COMPLEX WITH THE P8A VARIANT OF CC-CHEMOKINE MCP-1 Deposited 2002-08-29	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 D 24–99（76 aa）	Mutation：P8A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；14% PEG4000 200MM, SODIUM ACETATE, 100MM MAGNESIUM CHLORIDE, pH 4.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.282
1ML0 VIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS68 IN COMPLEX WITH THE P8A VARIANT OF CC-CHEMOKINE MCP-1 Deposited 2002-08-29	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain D 24–99（76 aa）	Mutation：P8A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；14% PEG4000 200MM, SODIUM ACETATE, 100MM MAGNESIUM CHLORIDE, pH 4.10, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.282
2BDN Crystal structure of human MCP-1 bound to a blocking antibody, 11K2 Deposited 2005-10-20	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 A 24–99（76 aa） Fragment：monocyte chemotactic protein -1	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13% PEG 4000, 100 mM Hepes, pH 7.5, 30 mM glycl-glycl-glycine, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.53 Å R-free 0.277
2NZ1 Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The CC-Chemokine CCL2/MCP-1 Deposited 2006-11-22	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 D 24–99（76 aa） Chain E 24–99（76 aa）	Mutation：M87I Mutation：M87I	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；12% PEG 4000, 100 mM sodium acetate, 200 mM magnesium chloride, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.300
2NZ1 Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The CC-Chemokine CCL2/MCP-1 Deposited 2006-11-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain Y 24–99（76 aa）	Mutation：M87I	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.1；293 K；12% PEG 4000, 100 mM sodium acetate, 200 mM magnesium chloride, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.300
3IFD Human synthetic monocyte chemoattractant protein 1 (MCP-1) Deposited 2009-07-24	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 24–99（76 aa） Fragment：residues 24-99	Not recorded	K POTASSIUM ION × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M TRIS PH 8.5, 2.4 M K/NA PHOSPHATE, 2% PEG 400 CRYO CONDITIONS: 0.1 M TRIS PH 8.5, 2.2 M K/NA PHOSPHATE, 2% PEG 400, 17% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.255
4DN4 Crystal structure of the complex between cnto888 fab and mcp-1 mutant p8a Deposited 2012-02-08	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 × 3 PDB declaration: trimeric	Chain M 24–99（76 aa）	Mutation：P8A	ACT ACETATE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；1.8 M AMMONIUM SULFATE, 0.1 M ACETATE, CRYO CONDITIONS: 2.0 M AMMONIUM SULFATE, 0.1 M ACETATE PH 5.5, 25% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.80 Å R-free 0.266
4R8I High Resolution Structure of a Mirror-Image RNA Oligonucleotide Aptamer in Complex with the Chemokine CCL2 Deposited 2014-09-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 24–99（76 aa）	Not recorded	NA SODIUM ION × 1 SR STRONTIUM ION × 1 K POTASSIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；After thorough optimization of crystallization conditions needle shaped crystals (approx. 300x50x50um) could be obtained by mixing 1uL of the NOX-E36-CCL2 complex (in 20 mM HEPES pH 7.4, 100 mM NaCl, 5 mM KCl, 1 mM MgCl2, 1 mM CaCl2) with 1uL of a solution containing 40 mM Na cacodylate pH 5.5, 12 mM spermine tetrahydrochloride, 40 mM LiCl, 80 mM SrCl2 and 20 mM MgCl2 and subsequent vapor-diffusion equilibration against 1 mL of reservoir (35% (v/v) MPD, 5 mM KCl, 1 mM MgCl2 and 1 mM CaCl2). Crystals used for data collection grew within three weeks at 277K. VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.05 Å R-free 0.250
4ZK9 The chemokine binding protein of orf virus complexed with CCL2 Deposited 2015-04-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–99（76 aa） Fragment：UNP residues 17-99	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；0.2M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate tribasic dihydrate pH5.6, 2.0M ammonium citrate	Resolution 2.60 Å R-free 0.281
7SO0 Crystal Structure of the Engineered Tick Evasin EVA-P974(F31A) Complexed to Human Chemokine CCL2 Deposited 2021-10-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–99（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；293 K；0.1 M Na3 Cit 3.5 pH (Buffer) 25 %w/v PEG 3350 (Precipitant)	Resolution 1.74 Å R-free 0.202
7XA3 Cryo-EM structure of the CCL2 bound CCR2-Gi complex Deposited 2022-03-17	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 L 24–92（69 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8FJ0 Crystal Structure of the Tick Evasin EVA-AAM1001(Y44A) Complexed to Human Chemokine CCL2 Deposited 2022-12-18	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 24–99（76 aa） Chain E 24–99（76 aa） Chain F 24–99（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；2 M NH4SO4, 0.1 M bis-tris, Ph 5.6	Resolution 2.91 Å R-free 0.284

13 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CCL2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–76； UniProt 24–99 Author chain B； PDBConstruct 1–76； UniProt 24–99

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1don
Deposition date deposition_date	1996-01-21
Structure title title	SOLUTION STRUCTURE OF THE MONOCYTE CHEMOATTRACTANT PROTEIN-1 DIMER USING HETERONUCLEAR, NMR, 20 STRUCTURES
Keywords keywords	HOMODIMER, HIGH RESOLUTION STRUCTURE, CHEMOATTRACTANT CYTOKINE, CHEMOKINE (CHEMOATTRACTANT CYTOKINE); CHEMOKINE (CHEMOATTRACTANT CYTOKINE)
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.80 Å
Radius of gyration Rg (electron density) rg_electron	18.81 Å
Forward intensity I(0) i0	1726740000.00
Molecular weight molecular_weight	347640.0 kDa
Excluded volume excluded_volume	434100 Å³
Envelope volume envelope_volume	47266 Å³
Hydration-shell volume shell_volume	18669 Å³
Envelope diameter envelope_diameter	71.0 Å
Shell Rg shell_rg	27.70 Å
Envelope Rg envelope_rg	22.49 Å
Shape Rg shape_rg	18.82 Å
Total Rg total_rg	18.91 Å
Total atoms total_atoms	49040
Residues n_residues	3040
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	62.1 Å
Rg (real space) rg_real	18.88 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	1.7270e+09
I(0) uncertainty (real space) i0_real_error	2.2100e+07
Rg (reciprocal space) rg_reciprocal	18.87 Å
I(0) (reciprocal space) i0_reciprocal	1727000000.0000
Solution quality estimate total_estimate	0.7738
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	16.2 Å
Skewness Skewness skewness	0.302
Kurtosis Kurtosis kurtosis	-0.728
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1092000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.759; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.782; Smooth: 0.000

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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_id	d1dona_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

Domain ID domain_id	d1donb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

CATH v4.4 (2 domains)

Domain ID domain_id	1donA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1donB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	MCP-1
Molecular weight formula_weight	8699.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	49040

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

SOLUTION STRUCTURE OF THE MONOCYTE CHEMOATTRACTANT PROTEIN-1 DIMER USING HETERONUCLEAR, NMR, 20 STRUCTURES

1. Protein Identity and Related Structures Protein Identity & Related Structures

MCP-1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/do/1don/1don.fit
pddf	/app/data/pr_computation/do/1don/1don.pr.out
profile	/app/data/saxs_computation/do/1don/1don.dat