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- PDB-9sop: Tissue inhibitor of metalloproteinase-1 (TIMP-1) -

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Basic information

Entry
Database: PDB / ID: 9sop
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 / 3,6,9,12,15-PENTAOXAHEPTADECANE / DI(HYDROXYETHYL)ETHER / Metalloproteinase inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)42,77014
Polymers41,4662
Non-polymers1,30512
Water1,47782
1
A: Metalloproteinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3435
Polymers20,7331
Non-polymers6104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metalloproteinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4289
Polymers20,7331
Non-polymers6958
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.229, 44.241, 90.53
Angle α, β, γ (deg.)90, 99.06, 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: LEU / End label comp-ID: LEU / Auth seq-ID: 1 - 179 / Label seq-ID: 1 - 179

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

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

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 6 types, 94 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-P3G / 3,6,9,12,15-PENTAOXAHEPTADECANE


Mass: 250.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O5
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 0.2 M Lithium Citrate tribasic tetrahydrate, 20% PEG 3350, 15% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92205 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 7, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92205 Å / Relative weight: 1
ReflectionResolution: 1.95→45.85 Å / Num. obs: 28422 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.033 / Rrim(I) all: 0.061 / Χ2: 0.84 / Net I/σ(I): 16.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.94-45.855.60.03830.23290.9980.0250.0450.8899.1
1.95-250.2384.219980.980.1770.2980.71100

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Processing

Software
NameVersionClassification
Aimless0.8.2data scaling
DIALS3.dev.1285-g5310fec54data reduction
gemmi0.7.1data extraction
REFMAC5.8.0431 (refmacat 0.4.105)refinement
Aimless0.8.2data scaling
DIALS3.dev.1285-g5310fec54data reduction
gemmi0.7.1data extraction
REFMAC5.8.0431 (refmacat 0.4.105)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→44.74 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.779 / SU ML: 0.107 / Cross valid method: FREE R-VALUE / ESU R: 0.167 / ESU R Free: 0.15
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1396 4.914 %RANDOM
Rwork0.1914 27011 --
all0.193 ---
obs-28407 99.979 %-
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: 37.585 Å2
Baniso -1Baniso -2Baniso -3
1-2.544 Å20 Å20.228 Å2
2--1.03 Å2-0 Å2
3----3.471 Å2
Refinement stepCycle: LAST / Resolution: 1.95→44.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2793 0 81 82 2956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122946
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162727
X-RAY DIFFRACTIONr_angle_refined_deg2.1331.8193983
X-RAY DIFFRACTIONr_angle_other_deg0.891.7356296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1325353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.203518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03510469
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.31210123
X-RAY DIFFRACTIONr_chiral_restr0.1350.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023381
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02687
X-RAY DIFFRACTIONr_nbd_refined0.1910.2446
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.22339
X-RAY DIFFRACTIONr_nbtor_refined0.170.21368
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21550
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.285
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2940.228
X-RAY DIFFRACTIONr_nbd_other0.2160.2136
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0940.211
X-RAY DIFFRACTIONr_mcbond_it4.153.3771421
X-RAY DIFFRACTIONr_mcbond_other4.1493.3771421
X-RAY DIFFRACTIONr_mcangle_it5.5036.051771
X-RAY DIFFRACTIONr_mcangle_other5.5036.0511772
X-RAY DIFFRACTIONr_scbond_it6.2023.9821525
X-RAY DIFFRACTIONr_scbond_other6.23.9821526
X-RAY DIFFRACTIONr_scangle_it8.2367.0162212
X-RAY DIFFRACTIONr_scangle_other8.2347.0162213
X-RAY DIFFRACTIONr_lrange_it9.79837.9973004
X-RAY DIFFRACTIONr_lrange_other9.79737.9983005
X-RAY DIFFRACTIONr_ncsr_local_group_10.1430.054958
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.142520.05008
12BX-RAY DIFFRACTIONLocal ncs0.142520.05008
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
1.95-2.0010.3421010.23119930.23620940.9370.9621000.208
2.001-2.0550.277930.21919250.22220190.9480.96699.95050.195
2.055-2.1150.268990.21418780.21719770.9490.9691000.194
2.115-2.180.261910.20318040.20618950.9550.9721000.183
2.18-2.2510.29800.19917940.20318740.9540.9731000.181
2.251-2.330.268770.20317190.20517960.9580.9741000.187
2.33-2.4180.248690.19216490.19417180.9590.9771000.179
2.418-2.5160.283950.18716030.19216980.960.9771000.174
2.516-2.6270.221850.19215000.19415850.9680.9771000.18
2.627-2.7550.232850.20414760.20615610.9620.9751000.196
2.755-2.9040.209740.18913920.1914660.9680.9771000.185
2.904-3.0790.225850.20413010.20513860.9640.9751000.205
3.079-3.290.289660.19412380.19913040.9530.9761000.201
3.29-3.5520.231590.18611500.18812090.9710.9791000.195
3.552-3.8890.204530.18810800.18911330.9710.981000.203
3.889-4.3440.158510.1649830.16410340.9870.9841000.185
4.344-5.0080.159440.1558630.1569070.9880.9871000.18
5.008-6.1150.219340.1867440.1887780.9740.9831000.213
6.115-8.5680.2330.2045730.2046060.9770.981000.232
8.568-44.740.353220.2413460.2463700.9320.96599.45950.541

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