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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 / negative regulation of endopeptidase activity / cellular response to acetaldehyde / negative regulation of membrane protein ectodomain proteolysis / negative regulation of trophoblast cell migration / connective tissue replacement involved in inflammatory response wound healing / metalloendopeptidase inhibitor activity / TGFBR3 PTM regulation / negative regulation of catalytic activity / cellular response to UV-A ...negative regulation of metallopeptidase activity / negative regulation of endopeptidase activity / cellular response to acetaldehyde / negative regulation of membrane protein ectodomain proteolysis / negative regulation of trophoblast cell migration / connective tissue replacement involved in inflammatory response wound healing / metalloendopeptidase inhibitor activity / TGFBR3 PTM regulation / negative regulation of catalytic activity / cellular response to UV-A / peptidase inhibitor activity / cellular response to peptide / regulation of integrin-mediated signaling pathway / cartilage development / Activation of Matrix Metalloproteinases / Interleukin-10 signaling / basement membrane / response to hormone / response to cytokine / platelet alpha granule lumen / cytokine activity / growth factor activity / Post-translational protein phosphorylation / response to peptide hormone / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / extracellular matrix / protease binding / Interleukin-4 and Interleukin-13 signaling / endoplasmic reticulum lumen / positive regulation of cell population proliferation / negative regulation of apoptotic process / : / 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 / TRIETHYLENE GLYCOL / 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: Acta Crystallogr D Struct Biol / Year: 2026
Title: The human TIMP-1 unbound structure provides a platform for fragment screening.
Authors: Shemy, A. / Van Broeckhoven, J. / Hellings, N. / Voet, A.
History
DepositionSep 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2025Provider: repository / Type: Initial release
Revision 2.0Apr 29, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / software / struct_asym / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_2 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr_ncs.rms_dev_position / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.R_factor_all / _refine_ls_shell.pdbx_fsc_free / _refine_ls_shell.pdbx_fsc_work / _refine_ls_shell.wR_factor_R_work / _software.classification / _software.name / _software.version / _struct_conn.pdbx_dist_value / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Description: Ligand identity
Details: Some ligands around the biomolecule were re-modelled, particularly those with weak or discontinuous electron density or multiple alternative conformations. These sites are not relevant to ...Details: Some ligands around the biomolecule were re-modelled, particularly those with weak or discontinuous electron density or multiple alternative conformations. These sites are not relevant to the biological or mechanistic focus of this study; however, they were adjusted to better reflect the observed crystallographic data and to avoid leaving unexplained positive difference density in the maps. Although this revision results in a slightly higher Rfree and a few additional outliers, it represents a more faithful and defensible interpretation of the experimental electron density. The updated model therefore prioritises accuracy of the map-to-model correspondence over global refinement statistics, which I believe is the scientifically more appropriate solution in this case.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,02916
Polymers40,6672
Non-polymers1,36214
Water1,74797
1
A: Metalloproteinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1438
Polymers20,3331
Non-polymers8107
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metalloproteinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8868
Polymers20,3331
Non-polymers5537
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 (eV)
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: 20333.402 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, 111 molecules

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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
REFMAC5.8.0431 (refmacat 0.4.105)refinement
REFMAC5.8.0431 (refmacat 0.4.105)refinement
Aimless0.8.2data scaling
DIALS3.dev.1285-g5310fec54data reduction
gemmi0.7.1data extraction
Aimless0.8.2data scaling
DIALS3.dev.1285-g5310fec54data reduction
gemmi0.7.1data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→44.74 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.265 / WRfactor Rwork: 0.205 / SU B: 3.839 / SU ML: 0.109 / Average fsc free: 0.957 / Average fsc work: 0.9728 / Cross valid method: FREE R-VALUE / ESU R: 0.172 / ESU R Free: 0.158 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 1396 4.914 %RANDOM
Rwork0.194 27011 --
all0.196 ---
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: 36.245 Å2
Baniso -1Baniso -2Baniso -3
1-2.477 Å20 Å20.217 Å2
2--1.086 Å2-0 Å2
3----3.456 Å2
Refinement stepCycle: LAST / Resolution: 1.95→44.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2793 0 90 97 2980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122970
X-RAY DIFFRACTIONr_angle_refined_deg1.9361.8244008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9135359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.495518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.610472
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.94910123
X-RAY DIFFRACTIONr_chiral_restr0.1570.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022210
X-RAY DIFFRACTIONr_nbd_refined0.2240.21075
X-RAY DIFFRACTIONr_nbtor_refined0.310.21967
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2118
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2660.2104
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1570.211
X-RAY DIFFRACTIONr_mcbond_it3.5733.3051427
X-RAY DIFFRACTIONr_mcangle_it4.9835.9081780
X-RAY DIFFRACTIONr_scbond_it5.1563.7921543
X-RAY DIFFRACTIONr_scangle_it7.1826.6942225
X-RAY DIFFRACTIONr_lrange_it9.3846.5014209
X-RAY DIFFRACTIONr_ncsr_local_group_10.1340.055025
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.134470.05008
12BX-RAY DIFFRACTIONLocal ncs0.134470.05008
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
1.95-2.0010.3561010.23219930.23720940.940.9631000.208
2.001-2.0550.3930.22319250.22620190.9490.96599.95050.198
2.055-2.1150.269990.21718780.2219770.9490.9681000.196
2.115-2.180.266910.21418040.21618950.9510.9691000.194
2.18-2.2510.288800.20317940.20718740.9540.9721000.184
2.251-2.330.281770.21417190.21717960.9530.9711000.198
2.33-2.4180.295690.20816490.21117180.9490.9731000.194
2.418-2.5160.271950.19516030.216980.9640.9761000.183
2.516-2.6270.256850.21415000.21615850.9560.9721000.201
2.627-2.7550.259850.22714760.22915610.9530.9691000.218
2.755-2.9040.276740.20813920.21214660.9480.9721000.205
2.904-3.0790.247850.20913010.21213860.9620.9731000.21
3.079-3.290.255660.19112380.19413040.9590.9771000.198
3.29-3.5520.238590.18311500.18512090.970.9791000.193
3.552-3.8890.21530.18310800.18511330.9740.981000.2
3.889-4.3440.174510.1629830.16210340.9840.9851000.181
4.344-5.0080.16440.1518630.1519070.9860.9871000.17
5.008-6.1150.202340.1747440.1757780.9760.9841000.203
6.115-8.5680.201330.2075730.2066060.9760.9791000.234
8.568-44.740.364220.2263460.2323700.9230.96899.45950.5

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