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1d2b

THE MMP-INHIBITORY, N-TERMINAL DOMAIN OF HUMAN TISSUE INHIBITOR OF METALLOPROTEINASES-1 (N-TIMP-1), SOLUTION NMR, 29 STRUCTURES

Method: SOLUTION NMR Dmax: 41.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Metalloproteinase inhibitor 1

Homo sapiens

UniProt P01033

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 24–149 Fragment：NTR domain, residues 24-149 No other associated polymer 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

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 1D2B Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 conditions 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 method 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 method 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 method 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 method 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 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 × 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 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 × 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 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 × 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 method 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 method 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
9SOQ Tissue inhibitor of Metalloproteinase 1 (TIMP-1) Deposited 2025-09-15 Different construct Different ligand/ion Different experimental method 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 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
9SOQ Tissue inhibitor of Metalloproteinase 1 (TIMP-1) Deposited 2025-09-15 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–207（184 aa）
Not recorded No recorded non-water small molecule 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
9SOS Tissue Inhibitor of Matrix Metalloproteinase-1 (TIMP-1) Deposited 2025-09-15 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–207（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 18 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 1–126； UniProt 24–149

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 1d2b

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d2b
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d2b
Deposition date deposition_date1999-09-22
Structure title titleTHE MMP-INHIBITORY, N-TERMINAL DOMAIN OF HUMAN TISSUE INHIBITOR OF METALLOPROTEINASES-1 (N-TIMP-1), SOLUTION NMR, 29 STRUCTURES
Keywords keywordsOB-FOLD, BETA BARREL, PROTEASE INHIBITOR, MMP INHIBITOR, HYDROLASE INHIBITOR; HYDROLASE INHIBITOR
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.39 Å
Radius of gyration Rg (electron density) rg_electron14.03 Å
Forward intensity I(0) i02382120000.00
Molecular weight molecular_weight413380.0 kDa
Excluded volume excluded_volume515510 ų
Envelope volume envelope_volume29175 ų
Hydration-shell volume shell_volume15555 ų
Envelope diameter envelope_diameter51.6 Å
Shell Rg shell_rg21.75 Å
Envelope Rg envelope_rg15.84 Å
Shape Rg shape_rg13.99 Å
Total Rg total_rg14.28 Å
Total atoms total_atoms57304
Residues n_residues3654
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 dmax41.4 Å
Rg (real space) rg_real14.30 Å
Rg uncertainty (real space) rg_real_error0.18 Å
I(0) (real space) i0_real2.3820e+09
I(0) uncertainty (real space) i0_real_error2.3370e+07
Rg (reciprocal space) rg_reciprocal14.31 Å
I(0) (reciprocal space) i0_reciprocal2382000000.0000
Solution quality estimate total_estimate0.8483
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary40.3 Å
Skewness Skewness skewness0.080
Kurtosis Kurtosis kurtosis-0.370
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha260400.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.185
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1d2ba_
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.3 — TIMP-like
Family Family familyb.40.3.1 — Tissue inhibitor of metalloproteinases, TIMP

CATH v4.4 (1 domains)

Domain ID domain_id1d2bA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily120 —
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8. Citations (2)

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9. Files and Curves (10)