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- PDB-1d2b: THE MMP-INHIBITORY, N-TERMINAL DOMAIN OF HUMAN TISSUE INHIBITOR O... -

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Basic information

Entry
Database: PDB / ID: 1d2b
TitleTHE MMP-INHIBITORY, N-TERMINAL DOMAIN OF HUMAN TISSUE INHIBITOR OF METALLOPROTEINASES-1 (N-TIMP-1), SOLUTION NMR, 29 STRUCTURES
ComponentsMetalloproteinase inhibitor 1
KeywordsHYDROLASE INHIBITOR / OB-FOLD / BETA BARREL / PROTEASE INHIBITOR / MMP INHIBITOR
Function / homology
Function and homology information


negative regulation of metallopeptidase activity / regulation of integrin-mediated signaling pathway / 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 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 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 endopeptidase activity / negative regulation of catalytic activity / cellular response to UV-A / cellular response to peptide / peptidase inhibitor activity / 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. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold ...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. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Metalloproteinase inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, CARTESIAN SIMULATED ANNEALING
AuthorsWu, B. / Arumugam, S. / Semenchenko, V. / Brew, K. / Van Doren, S.R.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: NMR structure of tissue inhibitor of metalloproteinases-1 implicates localized induced fit in recognition of matrix metalloproteinases.
Authors: Wu, B. / Arumugam, S. / Gao, G. / Lee, G.I. / Semenchenko, V. / Huang, W. / Brew, K. / Van Doren, S.R.
#1: Journal: J.Biomol.NMR / Year: 1999
Title: 1H, 13C and 15N Resonance Assignments and Secondary Structure of the N- Terminal Domain of Human Tissue Inhibitor of Metalloproteinases-1
Authors: Wu, B. / Arumugam, S. / Huang, W. / Brew, K. / Van Doren, S.R.
History
DepositionSep 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 23, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / database_2 ...citation / database_2 / entity / entity_name_com / entity_src_gen / pdbx_database_status / pdbx_nmr_refine / pdbx_nmr_representative / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _database_2.pdbx_DOI ..._citation.pdbx_database_id_PubMed / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_fragment / _entity_src_gen.pdbx_host_org_vector_type / _pdbx_database_status.status_code_cs / _pdbx_nmr_refine.details / _pdbx_nmr_refine.software_ordinal
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metalloproteinase inhibitor 1


Theoretical massNumber of molelcules
Total (without water)14,2691
Polymers14,2691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7400 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)29 / 120STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Representative

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Components

#1: Protein Metalloproteinase inhibitor 1 / TISSUE INHIBITOR OF METALLOPROTEINASES-1


Mass: 14269.307 Da / Num. of mol.: 1 / Fragment: NTR domain, residues 24-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: THIS IS THE FIRST 126 RESIDUES OF THE FULL LENGTH OF 184 RESIDUES NATURALLY OCCURRING IN HUMANS. THE 126 RESIDUE RECOMBINANT N-TERMINAL DOMAIN LACKS THE NATURAL N-LINKED GLYCOSYLATION OF ASN30 AND ASN78.
Cellular location: EXTRACELLULAR MATRIX / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P01033
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1223D TIME-SHARED NOESY-(13C,15N)-HSQC
1323D 13C FSCT-HSMQC-NOESY
1433D 13C NOESY-HMQC
NMR detailsText: 3D HNHB, 3D HACAHB-COSY, 2D HMQC-J, 3D COUPLED HCACO, 3D HNCA-J, {15N} SPIN- ECHO DIFFERENCE 13C CT-HSQC, {13CO} SPIN-ECHO DIFFERENCE 13C CT-HSQC, 2D HN(CG) , 2D HN(COCG), 15N IPAP-HSQC, 3D ...Text: 3D HNHB, 3D HACAHB-COSY, 2D HMQC-J, 3D COUPLED HCACO, 3D HNCA-J, {15N} SPIN- ECHO DIFFERENCE 13C CT-HSQC, {13CO} SPIN-ECHO DIFFERENCE 13C CT-HSQC, 2D HN(CG) , 2D HN(COCG), 15N IPAP-HSQC, 3D 13CA-COUPLED HNCO, 13C'-COUPLED IN-PHASE 15N HSQC

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Sample preparation

Details
Solution-IDContents
10.5 MM N-TIMP-1 U-15N
20.9 MM N-TIMP-1 U-15N,13C
30.7 MM N-TIMP-1 U-15N,13C
40.4 MM N-TIMP-1 16% 13C
50.4 MM N-TIMP-1 U-15N,13C
Sample conditionsIonic strength: 0.171 / pH: 6 / Pressure: AMBIENT / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
SYBYL TRIADV6.2 OR V.6.3TRIPOS INS., ST. LOUIS, MOprocessing
CNS0.6BRUNGER,A.T., ADAMS,P.D., CLORE,G.M., WARREN,G.L.structure solution
CNS0.6BRUNGER,A.T., ADAMS,P.D., CLORE,G.M., WARREN,G.L.refinement
RefinementMethod: TORSION ANGLE DYNAMICS, CARTESIAN SIMULATED ANNEALING
Software ordinal: 3
Details: Model 22 is closest to the average while Model 3 represents the conformer with the fewest violations
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 120 / Conformers submitted total number: 29

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