SAXSdb — 9soq

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

Metalloproteinase inhibitor 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 24–207	Not recorded	FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；293.15 K；0.2 Ammonium Sulphate, 0.1 M tri-sodium citrate, 25% PEG4000	Resolution 2.30 Å R-free 0.262
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 24–207	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.6；293.15 K；0.2 Ammonium Sulphate, 0.1 M tri-sodium citrate, 25% PEG4000	Resolution 2.30 Å R-free 0.262

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 9SOQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D2B THE MMP-INHIBITORY, N-TERMINAL DOMAIN OF HUMAN TISSUE INHIBITOR OF METALLOPROTEINASES-1 (N-TIMP-1), SOLUTION NMR, 29 STRUCTURES Deposited 1999-09-22	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–149（126 aa） Fragment：NTR domain, residues 24-149	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；293 K；Ionic strength (raw mmCIF value) 0.171；Pressure AMBIENT NMR sample composition 0.5 MM N-TIMP-1 U-15N NMR sample composition 0.9 MM N-TIMP-1 U-15N,13C NMR sample composition 0.7 MM N-TIMP-1 U-15N,13C NMR sample composition 0.4 MM N-TIMP-1 16% 13C NMR sample composition 0.4 MM N-TIMP-1 U-15N,13C	Resolution not provided
1OO9 Orientation in Solution of MMP-3 Catalytic Domain and N-TIMP-1 from Residual Dipolar Couplings Deposited 2003-03-03	Different construct 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 24–149（126 aa） Fragment：N-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.6；310 K；Ionic strength (raw mmCIF value) 20mM Tris-d11; 100 mM NaCl; 15 mM CaCl2; 3uM ZnCl2; 1mM Sodium Azide；Pressure ambient NMR measurement conditions pH 6.7；307 K；Ionic strength (raw mmCIF value) 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2;1mM Sodium Azide；Pressure ambient NMR sample composition 0.8mM MMP-3 U-15N, 13C; 0.8mM N-TIMP-1; 20mM Tris-d11; 100 mM NaCl; 15 mM CaCl2; 3uM ZnCl2; 1mM Sodium Azide; 93% H2O, 7% D2O \| 93% H2O/7% D2O NMR sample composition 0.5mM MMP-3 U-2H, 15N; 0.5mM N-TIMP-1; 20mM Tris-d11; 100 mM NaCl; 15 mM CaCl2; 3uM ZnCl2; 1mM Sodium Azide; 93% H2O, 7% D2O \| 93% H2O/7% D2O NMR sample composition 0.66mM N-TIMP-1 U-15N, 13C; 0.66mM MMP-3(E202Q); 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2; 1mM Sodium Azide; 93% H2O; 7% D2O \| 93% H2O/7% D2O NMR sample composition 0.3mM 98% 2H/15N N-TIMP-1; 0.3mM MMP-3 (E202Q); 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2; 1mM Sodium Azide; 93% H2O; 7% D2O \| 93% H2O/7% D2O NMR sample composition 0.3mM 98% 2H/15N N-TIMP-1; 0.3mM (15N-IV, 15N, 13C-L)MMP-3(E202Q); 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2; 1mM Sodium Azide; 93% H2O; 7% D2O \| 93% H2O/7% D2O NMR sample composition 0.3mM 98% 2H/15N N-TIMP-1; 0.3mM (15N-IV, 15N, 13C-L)MMP-3(E202Q); 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2; 1mM Sodium Azide; 93% H2O; 7% D2O 5% PEG(C12E6)/1-hexanol \| 93% H2O; 7% D2O 5% PEG(C12E6)/1-hexanol	Resolution not provided
1UEA MMP-3/TIMP-1 COMPLEX Deposited 1997-06-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–207（184 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1UEA MMP-3/TIMP-1 COMPLEX Deposited 1997-06-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 24–207（184 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
2J0T Crystal Structure of the Catalytic Domain of MMP-1 in Complex with the Inhibitory Domain of TIMP-1 Deposited 2006-08-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 24–149（126 aa） Fragment：N-TERMINAL INHIBITORY DOMAIN, RESIDUES 24-149	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；10% PEG 8000, 8% ETHYLENE GLYCOL, 0.1M HEPES (PH 7.5).	Resolution 2.54 Å R-free 0.275
2J0T Crystal Structure of the Catalytic Domain of MMP-1 in Complex with the Inhibitory Domain of TIMP-1 Deposited 2006-08-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 24–149（126 aa） Fragment：N-TERMINAL INHIBITORY DOMAIN, RESIDUES 24-149	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；10% PEG 8000, 8% ETHYLENE GLYCOL, 0.1M HEPES (PH 7.5).	Resolution 2.54 Å R-free 0.275
2J0T Crystal Structure of the Catalytic Domain of MMP-1 in Complex with the Inhibitory Domain of TIMP-1 Deposited 2006-08-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 24–149（126 aa） Fragment：N-TERMINAL INHIBITORY DOMAIN, RESIDUES 24-149	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；10% PEG 8000, 8% ETHYLENE GLYCOL, 0.1M HEPES (PH 7.5).	Resolution 2.54 Å R-free 0.275
3MA2 Complex membrane type-1 matrix metalloproteinase (MT1-MMP) with tissue inhibitor of metalloproteinase-1 (TIMP-1) Deposited 2010-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 24–148（125 aa） Fragment：Residues 24-148	Mutation：V27A,P29V,T121L	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；292 K；100 mM Bis-Tris pH 5.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.05 Å R-free 0.247
3MA2 Complex membrane type-1 matrix metalloproteinase (MT1-MMP) with tissue inhibitor of metalloproteinase-1 (TIMP-1) Deposited 2010-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–148（125 aa） Fragment：Residues 24-148	Mutation：V27A,P29V,T121L	CA CALCIUM ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；292 K；100 mM Bis-Tris pH 5.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.05 Å R-free 0.247
3V96 Complex of matrix metalloproteinase-10 catalytic domain (MMP-10cd) with tissue inhibitor of metalloproteinases-1 (TIMP-1) Deposited 2011-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 24–207（184 aa） Fragment：unp residues 24-207	Mutation：N30A	PO4 PHOSPHATE ION × 2 ZN ZINC ION × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；298 K；0.1 M sodium dihydrogen phosphate solution, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.266
6MAV Complex of tissue inhibitor of metalloproteinase-1 (TIMP-1) mutant L34G with matrix metalloproteinase-3 catalytic domain (MMP-3cd) Deposited 2018-08-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–207（184 aa）	Mutation：L34G	CA CALCIUM ION × 3 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1 M Ammonium Acetate 0.1 M Bis-Tris: HCl, pH 5.5, 17 % (w/v) PEG 10,000	Resolution 2.37 Å R-free 0.298
6N9D Complex of tissue inhibitor of metalloproteinases-1 (TIMP-1) mutant (L34G/L133P/L151C/G154A) with matrix metalloproteinase-3 catalytic domain (MMP-3cd) Deposited 2018-12-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–207（184 aa）	Not recorded	CA CALCIUM ION × 3 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Sodium Acetate, 0.1 M Sodium Cacodylate: HCl, pH 6.5 18 % (w/v) PEG 8000	Resolution 2.67 Å R-free 0.258
7S7L Complex of tissue inhibitor of metalloproteinases-1 (TIMP-1) mutant (L34G/M66S/E67Y/L133N/S155L) with matrix metalloproteinase-3 catalytic domain (MMP-3cd) Deposited 2021-09-16	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–207（184 aa）	Mutation：L34G, M66S, E67Y, L133N, S155L	CA CALCIUM ION × 3 ZN ZINC ION × 2 CL CHLORIDE ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 SO4 SULFATE ION × 1 GOL GLYCEROL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；310 K；0.2M ammonium sulfate, 0.1M Bis-Tris pH 6.5, 25% w/v PEG 3350 Anatrace-Microlytic Top96 #65	Resolution 2.34 Å R-free 0.239
7S7M Complex of tissue inhibitor of metalloproteinases-1 (TIMP-1) mutant (L34G/M66D/T98G/P131S/Q153N) with matrix metalloproteinase-3 catalytic domain (MMP-3cd) Deposited 2021-09-16	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–207（184 aa）	Mutation：L34G, M66D, T98G, P131S, Q153N	CA CALCIUM ION × 3 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；310 K；0.1 M ammonium acetate, 0.1 M Bis-Tris-HCl, pH 5.5, 17% w/v PEG10000	Resolution 3.00 Å R-free 0.248
9SOP Tissue inhibitor of metalloproteinase-1 (TIMP-1) Deposited 2025-09-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–203（180 aa）	Not recorded	GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 3 FLC CITRATE ANION × 1 P3G 3,6,9,12,15-PENTAOXAHEPTADECANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293.15 K；0.2 M Lithium Citrate tribasic tetrahydrate, 20% PEG 3350, 15% Glycerol	Resolution 1.95 Å R-free 0.239
9SOP Tissue inhibitor of metalloproteinase-1 (TIMP-1) Deposited 2025-09-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 24–203（180 aa）	Not recorded	GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 5 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293.15 K；0.2 M Lithium Citrate tribasic tetrahydrate, 20% PEG 3350, 15% Glycerol	Resolution 1.95 Å R-free 0.239
9SOS Tissue Inhibitor of Matrix Metalloproteinase-1 (TIMP-1) Deposited 2025-09-15	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–207（184 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293.15 K；0.2 M Lithium Citrate tribasic tetrahydrate, 20% PEG3350	Resolution 2.00 Å R-free 0.255

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

View Construct and Data Evidence

UniProt name	TIMP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–184； UniProt 24–207 Author chain B； PDBConstruct 1–184； UniProt 24–207

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	9soq
Deposition date deposition_date	2025-09-15
Structure title title	Tissue inhibitor of Metalloproteinase 1 (TIMP-1)
Keywords keywords	Hydrolase Inhibitor, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	25.50 Å
Radius of gyration Rg (electron density) rg_electron	24.90 Å
Forward intensity I(0) i0	27061600.00
Molecular weight molecular_weight	39139.0 kDa
Excluded volume excluded_volume	48648 Å³
Envelope volume envelope_volume	61767 Å³
Hydration-shell volume shell_volume	21763 Å³
Envelope diameter envelope_diameter	93.3 Å
Shell Rg shell_rg	30.51 Å
Envelope Rg envelope_rg	25.04 Å
Shape Rg shape_rg	24.86 Å
Total Rg total_rg	25.74 Å
Total atoms total_atoms	2742
Residues n_residues	359
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	89.6 Å
Rg (real space) rg_real	25.58 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	2.7060e+07
I(0) uncertainty (real space) i0_real_error	4.0790e+05
Rg (reciprocal space) rg_reciprocal	25.56 Å
I(0) (reciprocal space) i0_reciprocal	27060000.0000
Solution quality estimate total_estimate	0.7101
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.0 Å
Skewness Skewness skewness	0.398
Kurtosis Kurtosis kurtosis	-0.334
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2948000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 0.315; Positv: 1.000; Valcen: 0.891; Smooth: 0.957

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Metalloproteinase inhibitor 1
Molecular weight formula_weight	20732.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2826

CTCVPPHPQTAFCNSDLVIRAKFVGTPEVNQTTLYQRYEIKMTKMYKGFQALGDAADIRFVYTPAMESVCGYFHRSHNRSEEFLIAGKLQDGLLHITTCSFVAPWNSLSLAQRRGFTKTYTVGCEECTVFPCLSIPCKLQSGTHCLWTDQLLQGSEKGFQSRHLACLPREPGLCTWQSLRSQIA

来源 Source

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	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	84

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8. Citations (1)

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Unit-cell length a length_a	48.979 Å
Unit-cell length b length_b	45.542 Å
Unit-cell length c length_c	90.347 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.88 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	45.840 Å
R factor r_factor	—
R_work r_work	0.2101
R_free r_free	0.2621

fit	/app/data/saxs_computation/so/9soq/9soq.fit
pddf	/app/data/pr_computation/so/9soq/9soq.pr.out
profile	/app/data/saxs_computation/so/9soq/9soq.dat

Tissue inhibitor of Metalloproteinase 1 (TIMP-1)

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

Metalloproteinase inhibitor 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

Refinement Refinement

Diffraction experiment Diffraction