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- PDB-9soq: Tissue inhibitor of Metalloproteinase 1 (TIMP-1) -

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Basic information

Entry
Database: PDB / ID: 9soq
TitleTissue inhibitor of Metalloproteinase 1 (TIMP-1)
ComponentsMetalloproteinase inhibitor 1
KeywordsHYDROLASE / Hydrolase Inhibitor
Function / homology
Function and homology information


negative regulation of metallopeptidase activity / regulation of integrin-mediated signaling pathway / negative regulation of trophoblast cell migration / negative regulation of membrane protein ectodomain proteolysis / connective tissue replacement involved in inflammatory response wound healing / metalloendopeptidase inhibitor activity / TGFBR3 PTM regulation / negative regulation of endopeptidase activity / negative regulation of catalytic activity / cellular response to UV-A ...negative regulation of metallopeptidase activity / regulation of integrin-mediated signaling pathway / negative regulation of trophoblast cell migration / negative regulation of membrane protein ectodomain proteolysis / connective tissue replacement involved in inflammatory response wound healing / metalloendopeptidase inhibitor activity / TGFBR3 PTM regulation / negative regulation of endopeptidase activity / negative regulation of catalytic activity / cellular response to UV-A / peptidase inhibitor activity / cellular response to peptide / cartilage development / Activation of Matrix Metalloproteinases / Interleukin-10 signaling / basement membrane / response to hormone / response to cytokine / extracellular matrix / platelet alpha granule lumen / cytokine activity / Post-translational protein phosphorylation / growth factor activity / response to peptide hormone / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / protease binding / Interleukin-4 and Interleukin-13 signaling / endoplasmic reticulum lumen / positive regulation of cell population proliferation / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / zinc ion binding
Similarity search - Function
Protease inhibitor I35 (TIMP) / Proteinase inhibitor I35b (TIMP), C-terminal / Tissue inhibitor of metalloproteinase, conserved site / Tissue inhibitor of metalloproteinase / Tissue inhibitors of metalloproteinases signature. / Tissue inhibitor of metalloproteinase family. / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold
Similarity search - Domain/homology
CITRATE ANION / Metalloproteinase inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShemy, A. / Voet, A.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1S11123N Belgium
Research Foundation - Flanders (FWO)1S11125N Belgium
CitationJournal: To Be Published
Title: Tissue inhibitor of Metalloproteinase 1 (TIMP-1)
Authors: Shemy, A. / Voet, A.
History
DepositionSep 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metalloproteinase inhibitor 1
B: Metalloproteinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6553
Polymers41,4662
Non-polymers1891
Water1,51384
1
A: Metalloproteinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9222
Polymers20,7331
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metalloproteinase inhibitor 1


Theoretical massNumber of molelcules
Total (without water)20,7331
Polymers20,7331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.979, 45.542, 90.347
Angle α, β, γ (deg.)90, 99.876, 90
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 1 - 178 / Label seq-ID: 1 - 178

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Metalloproteinase inhibitor 1 / Erythroid-potentiating activity / EPA / Fibroblast collagenase inhibitor / Collagenase inhibitor / ...Erythroid-potentiating activity / EPA / Fibroblast collagenase inhibitor / Collagenase inhibitor / Tissue inhibitor of metalloproteinases 1 / TIMP-1


Mass: 20732.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMP1, CLGI, TIMP / Production host: Homo sapiens (human) / References: UniProt: P01033
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 Ammonium Sulphate, 0.1 M tri-sodium citrate, 25% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.3→45.84 Å / Num. obs: 17537 / % possible obs: 99.1 % / Redundancy: 3.5 % / CC1/2: 0.983 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.144 / Rrim(I) all: 0.21 / Χ2: 0.9 / Net I/σ(I): 4.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.91-45.843.20.062113390.9850.0610.0870.6299.2
2.3-2.383.60.931.317070.6640.8761.280.999.9

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Processing

Software
NameVersionClassification
Aimless0.7.15data scaling
DIALS3.18.0-gbecf27540-releasedata reduction
gemmi0.7.1data extraction
REFMAC5.8.0431 (refmacat 0.4.105)refinement
Aimless0.7.15data scaling
DIALS3.18.0-gbecf27540-releasedata reduction
gemmi0.7.1data extraction
REFMAC5.8.0431 (refmacat 0.4.105)refinement
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→45.84 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / SU B: 11.028 / SU ML: 0.243 / Cross valid method: FREE R-VALUE / ESU R: 0.362 / ESU R Free: 0.255 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.2621 929 5.311 %RANDOM
Rwork0.2101 16563 --
all0.213 ---
obs-17492 98.736 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.434 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.201 Å2
2--3.812 Å20 Å2
3----3.641 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2729 0 13 84 2826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122826
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.8043858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.995357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.678512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41610421
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.72910113
X-RAY DIFFRACTIONr_chiral_restr0.1430.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022174
X-RAY DIFFRACTIONr_nbd_refined0.2260.21076
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21888
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2119
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.230.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1350.210
X-RAY DIFFRACTIONr_mcbond_it4.3524.0771434
X-RAY DIFFRACTIONr_mcangle_it6.747.3191789
X-RAY DIFFRACTIONr_scbond_it4.8354.1541392
X-RAY DIFFRACTIONr_scangle_it7.0887.5182069
X-RAY DIFFRACTIONr_lrange_it10.72249.3774036
X-RAY DIFFRACTIONr_ncsr_local_group_10.1270.054991
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.127140.05009
12BX-RAY DIFFRACTIONLocal ncs0.127140.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.3-2.360.351920.33811710.33912710.9140.90799.37060.336
2.36-2.4240.372550.32411890.32612480.9050.91999.67950.327
2.424-2.4940.347690.3211570.32212350.9210.92699.27130.322
2.494-2.5710.427550.311660.30512290.8870.93699.34910.292
2.571-2.6550.324490.27410860.27611420.9220.9599.3870.27
2.655-2.7480.325690.2710450.27311170.9260.95399.73140.267
2.748-2.8510.327500.25510320.25810840.930.9699.81550.25
2.851-2.9670.308470.2459830.24710370.9290.96199.3250.235
2.967-3.0980.366470.2369500.24310060.9180.96599.10540.227
3.098-3.2490.267530.1998980.2029630.9540.97698.75390.193
3.249-3.4240.252370.2058450.2079020.9660.97697.78270.198
3.424-3.630.242460.1857790.1888620.9560.98295.70770.181
3.63-3.8790.209500.1737140.1758300.9750.98592.04820.17
3.879-4.1870.237420.1617070.1657750.9690.98696.64520.16
4.187-4.5830.214410.1416550.1456970.9740.98999.85650.14
4.583-5.1180.157390.1365990.1376380.9860.9881000.136
5.118-5.8970.238260.175380.1735640.9630.9831000.169
5.897-7.1930.262260.1924680.1964940.9670.9821000.189
7.193-10.0490.193240.23580.23850.9830.98399.22080.202
10.049-45.840.254120.2312230.2322350.9790.9761000.237

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