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- PDB-5n5j: Human MMP12 in complex with 3-(5-(1,2-dithiolan-3-yl)pentanamido)... -

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Basic information

Entry
Database: PDB / ID: 5n5j
TitleHuman MMP12 in complex with 3-(5-(1,2-dithiolan-3-yl)pentanamido)propane-1-sulfonate
ComponentsMacrophage metalloelastase
KeywordsHYDROLASE / MMP12 / lipoic acid / inhibitor
Function / homology
Function and homology information


macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development ...macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / positive regulation of interferon-alpha production / core promoter sequence-specific DNA binding / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / cellular response to virus / metalloendopeptidase activity / protein import into nucleus / endopeptidase activity / sequence-specific DNA binding / serine-type endopeptidase activity / calcium ion binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm
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-8NT / ACETOHYDROXAMIC ACID / Macrophage metalloelastase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCalderone, V.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Lipoyl-Homotaurine Derivative (ADM_12) Reverts Oxaliplatin-Induced Neuropathy and Reduces Cancer Cells Malignancy by Inhibiting Carbonic Anhydrase IX (CAIX).
Authors: Fragai, M. / Comito, G. / Di Cesare Mannelli, L. / Gualdani, R. / Calderone, V. / Louka, A. / Richichi, B. / Francesconi, O. / Angeli, A. / Nocentini, A. / Gratteri, P. / Chiarugi, P. / ...Authors: Fragai, M. / Comito, G. / Di Cesare Mannelli, L. / Gualdani, R. / Calderone, V. / Louka, A. / Richichi, B. / Francesconi, O. / Angeli, A. / Nocentini, A. / Gratteri, P. / Chiarugi, P. / Ghelardini, C. / Tadini-Buoninsegni, F. / Supuran, C.T. / Nativi, C.
History
DepositionFeb 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1388
Polymers17,4841
Non-polymers6547
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-59 kcal/mol
Surface area7900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.926, 60.470, 53.844
Angle α, β, γ (deg.)90.00, 114.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-470-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Macrophage metalloelastase / MME / Macrophage elastase / hME / Matrix metalloproteinase-12 / MMP-12


Mass: 17484.475 Da / Num. of mol.: 1 / Mutation: F171D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP12, HME / Production host: Escherichia coli (E. coli) / References: UniProt: P39900, macrophage elastase

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Non-polymers , 5 types, 148 molecules

#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.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-HAE / ACETOHYDROXAMIC ACID


Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2 / Comment: inhibitor, medication*YM
#5: Chemical ChemComp-8NT / 3-[5-[(3~{S})-1,2-dithiolan-3-yl]pentanoylamino]propane-1-sulfonic acid


Mass: 327.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H21NO4S3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris-HCl, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Dec 15, 2015
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→24.49 Å / Num. obs: 12916 / % possible obs: 93.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.031 / Net I/σ(I): 5.6
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 291 / Rpim(I) all: 0.175 / % possible all: 77.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y93

1y93


Resolution: 1.8→24.29 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.364 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R Free: 0.124 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19533 660 5.1 %RANDOM
Rwork0.12545 ---
obs0.12909 12255 93.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.609 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0 Å2-0.02 Å2
2--0.04 Å20 Å2
3---0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.8→24.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1238 0 29 141 1408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191298
X-RAY DIFFRACTIONr_bond_other_d0.0030.021141
X-RAY DIFFRACTIONr_angle_refined_deg1.9791.9321758
X-RAY DIFFRACTIONr_angle_other_deg1.14832639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5845157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34123.17563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.10515188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.014157
X-RAY DIFFRACTIONr_chiral_restr0.130.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021474
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02296
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3031.076632
X-RAY DIFFRACTIONr_mcbond_other2.2841.558630
X-RAY DIFFRACTIONr_mcangle_it2.4681.6787
X-RAY DIFFRACTIONr_mcangle_other2.482.161788
X-RAY DIFFRACTIONr_scbond_it4.2961.446666
X-RAY DIFFRACTIONr_scbond_other3.994663
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.712.015972
X-RAY DIFFRACTIONr_long_range_B_refined3.91914.3441537
X-RAY DIFFRACTIONr_long_range_B_other3.85214.0291513
X-RAY DIFFRACTIONr_rigid_bond_restr8.03431298
X-RAY DIFFRACTIONr_sphericity_free19.178586
X-RAY DIFFRACTIONr_sphericity_bonded10.54951323
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 13 -
Rwork0.192 409 -
obs--42.24 %
Refinement TLS params.Method: refined / Origin x: 10.57 Å / Origin y: 0.6598 Å / Origin z: 10.2558 Å
111213212223313233
T0.0253 Å20.0027 Å2-0.0015 Å2-0.0037 Å2-0.0019 Å2--0.0033 Å2
L0.4025 °2-0.2408 °2-0.0499 °2-0.229 °20.1269 °2--0.4884 °2
S0.0006 Å °0.0149 Å °-0.0211 Å °-0.0212 Å °-0.0142 Å °0.0254 Å °-0.0033 Å °0.0038 Å °0.0136 Å °

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