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- PDB-2jnp: Solution structure of matrix metalloproteinase 3 (MMP-3) in the p... -

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Basic information

Entry
Database: PDB / ID: 2jnp
TitleSolution structure of matrix metalloproteinase 3 (MMP-3) in the presence of N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid (NNGH)
ComponentsMatrix metalloproteinase-3
KeywordsHYDROLASE / metalloproteinase / MMP
Function / homology
Function and homology information


stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / cellular response to nitric oxide ...stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / cellular response to nitric oxide / negative regulation of reactive oxygen species metabolic process / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cell migration / EGFR Transactivation by Gastrin / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / cellular response to amino acid stimulus / protein catabolic process / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / peptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / Extra-nuclear estrogen signaling / serine-type endopeptidase activity / innate immune response / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytosol
Similarity search - Function
Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin ...Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NGH / Stromelysin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsAlcaraz, L.A. / Banci, L. / Bertini, I. / Cantini, F. / Donaire, A. / Gonnelli, L.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2007
Title: Matrix metalloproteinase-inhibitor interaction: the solution structure of the catalytic domain of human matrix metalloproteinase-3 with different inhibitors
Authors: Alcaraz, L.A. / Banci, L. / Bertini, I. / Cantini, F. / Donaire, A. / Gonnelli, L.
History
DepositionJan 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.deposit_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix metalloproteinase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5706
Polymers18,0431
Non-polymers5275
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1010 Å2
ΔGint-88 kcal/mol
Surface area8840 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 400target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Matrix metalloproteinase-3 / MMP-3 / Stromelysin-1 / Transin-1 / SL-1


Mass: 18043.037 Da / Num. of mol.: 1 / Fragment: residues 88-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP3, STMY1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL(DE3) / References: UniProt: P08254, stromelysin 1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NGH / N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID


Mass: 316.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20N2O5S

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1232D 1H-15N HSQC
1322D 1H-13C HSQC
1423D CBCA(CO)NH
1523D HN(CA)CB
1623D (H)CCH-TOCSY
1733D 1H-15N NOESY
1823D 1H-13C NOESY
1923D HNCA
11023D HN(CO)CA
1112Filtered NOESY
11223D HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM MMP3, 20 mM TRIS, 300 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-98% 13C; U-98% 15N] MMP3, 20 mM TRIS, 300 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-99% 15N] MMP3, 20 mM TRIS, 300 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMMP31
20 mMTRIS1
300 mMsodium chloride1
1 mMMMP3[U-98% 13C; U-98% 15N]2
20 mMTRIS2
300 mMsodium chloride2
1 mMMMP3[U-99% 15N]3
20 mMTRIS3
300 mMsodium chloride3
Sample conditionsIonic strength: Tris 0.02, NaCl 3 / pH: 8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
XEASYBartels et al.data analysis
CARA1.2Keller and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollrefinement
Sparky3.11Goddardchemical shift assignment
Sparky3.11Goddarddata analysis
CSI2Wishart, D.S. and B.D. Sykesstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 25

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