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- PDB-5ue4: proMMP-9desFnII complexed to JNJ0966 INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 5ue4
TitleproMMP-9desFnII complexed to JNJ0966 INHIBITOR
ComponentsMatrix metalloproteinase-9
KeywordsHYDROLASE/HYDROLASE INHIBITOR / prommp9 / zymogen / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases ...gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / endodermal cell differentiation / positive regulation of release of cytochrome c from mitochondria / response to amyloid-beta / macrophage differentiation / Collagen degradation / EPH-ephrin mediated repulsion of cells / collagen catabolic process / extracellular matrix disassembly / ephrin receptor signaling pathway / positive regulation of DNA binding / negative regulation of intrinsic apoptotic signaling pathway / embryo implantation / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to cadmium ion / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of receptor binding / skeletal system development / Signaling by SCF-KIT / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / cell migration / tertiary granule lumen / peptidase activity / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / cellular response to lipopolysaccharide / ficolin-1-rich granule lumen / Extra-nuclear estrogen signaling / positive regulation of protein phosphorylation / positive regulation of apoptotic process / serine-type endopeptidase activity / apoptotic process / Neutrophil degranulation / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding
Similarity search - Function
Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site ...Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / 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 / Kringle-like fold / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5XQ / Matrix metalloproteinase-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsAlexander, R.S. / Spurlino, J. / Milligan, C.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Discovery of a highly selective chemical inhibitor of matrix metalloproteinase-9 (MMP-9) that allosterically inhibits zymogen activation.
Authors: Scannevin, R.H. / Alexander, R. / Haarlander, T.M. / Burke, S.L. / Singer, M. / Huo, C. / Zhang, Y.M. / Maguire, D. / Spurlino, J. / Deckman, I. / Carroll, K.I. / Lewandowski, F. / Devine, E. ...Authors: Scannevin, R.H. / Alexander, R. / Haarlander, T.M. / Burke, S.L. / Singer, M. / Huo, C. / Zhang, Y.M. / Maguire, D. / Spurlino, J. / Deckman, I. / Carroll, K.I. / Lewandowski, F. / Devine, E. / Dzordzorme, K. / Tounge, B. / Milligan, C. / Bayoumy, S. / Williams, R. / Schalk-Hihi, C. / Leonard, K. / Jackson, P. / Todd, M. / Kuo, L.C. / Rhodes, K.J.
History
DepositionDec 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix metalloproteinase-9
B: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,13615
Polymers53,0252
Non-polymers1,11113
Water5,693316
1
A: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8607
Polymers26,5131
Non-polymers3476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2768
Polymers26,5131
Non-polymers7647
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Matrix metalloproteinase-9
hetero molecules

B: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,13615
Polymers53,0252
Non-polymers1,11113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2000 Å2
ΔGint-86 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.820, 72.945, 77.537
Angle α, β, γ (deg.)90.00, 106.91, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-551-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Matrix metalloproteinase-9 / / MMP-9 / 92 kDa gelatinase / 92 kDa type IV collagenase / Gelatinase B / GELB


Mass: 26512.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP9, CLG4B / Production host: Escherichia coli (E. coli) / References: UniProt: P14780, gelatinase B

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Non-polymers , 5 types, 329 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-5XQ / ~{N}-[5-[2-[(2-methoxyphenyl)amino]-1,3-thiazol-4-yl]-4-methyl-1,3-thiazol-2-yl]ethanamide


Mass: 360.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16N4O2S2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 25% PEG 8K 1% glycerol 0.2 M ammonium sulfate 100 mM NaCacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→43 Å / Num. obs: 44322 / % possible obs: 99.7 % / Redundancy: 3.25 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 10.5

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Processing

Software
NameClassification
PHENIXrefinement
d*TREKdata scaling
RefinementResolution: 1.8→43 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2243 2000 4.51 %
Rwork0.1991 --
obs0.2003 44303 99.68 %
Displacement parametersBiso mean: 32.84 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3562 0 39 316 3917

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