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- PDB-5i12: Crystal structure of the catalytic domain of MMP-9 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5i12
TitleCrystal structure of the catalytic domain of MMP-9 in complex with a selective sugar-conjugated arylsulfonamide carboxylate water-soluble inhibitor (DC27).
ComponentsMatrix metalloproteinase-9,Matrix metalloproteinase-9
KeywordsHYDROLASE / Inhibitor / complex / glycoconjugate / metalloprotease
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 / collagen catabolic process / EPH-ephrin mediated repulsion of cells / extracellular matrix disassembly / ephrin receptor signaling pathway / positive regulation of DNA binding / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / collagen binding / cellular response to cadmium ion / embryo implantation / 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 / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / endopeptidase activity / 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 / zinc ion binding / extracellular exosome / 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. / 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-H27 / Matrix metalloproteinase-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsStura, E.A. / Rosalia, L. / Cuffaro, D. / Tepshi, L. / Ciccone, L. / Rossello, A.
CitationJournal: Chemmedchem / Year: 2016
Title: Sugar-Based Arylsulfonamide Carboxylates as Selective and Water-Soluble Matrix Metalloproteinase-12 Inhibitors.
Authors: Nuti, E. / Cuffaro, D. / D'Andrea, F. / Rosalia, L. / Tepshi, L. / Fabbi, M. / Carbotti, G. / Ferrini, S. / Santamaria, S. / Camodeca, C. / Ciccone, L. / Orlandini, E. / Nencetti, S. / ...Authors: Nuti, E. / Cuffaro, D. / D'Andrea, F. / Rosalia, L. / Tepshi, L. / Fabbi, M. / Carbotti, G. / Ferrini, S. / Santamaria, S. / Camodeca, C. / Ciccone, L. / Orlandini, E. / Nencetti, S. / Stura, E.A. / Dive, V. / Rossello, A.
History
DepositionFeb 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,81810
Polymers17,5721
Non-polymers1,2469
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-19 kcal/mol
Surface area8050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.560, 39.560, 163.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

21A-517-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 17571.518 Da / Num. of mol.: 1
Fragment: UNP residues 113-216,UNP residues 392-444,UNP residues 113-216,UNP residues 392-444
Source method: isolated from a genetically manipulated source
Details: MMP-9 catalytic domain without fibronectin type II domains
Source: (gene. exp.) Homo sapiens (human) / Cell: Neutrophil / Gene: MMP9, CLG4B / Production host: Escherichia coli (E. coli) / References: UniProt: P14780, gelatinase B

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Non-polymers , 7 types, 126 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-H27 / (2R)-2-[{(E)-2-[({(2R,3R,4R,5S,6R)-3-(acetylamino)-4,5-bis(acetyloxy)-6-[(acetyloxy)methyl]tetrahydro-2H-pyran-2-yl}carbamothioyl)amino]ethenyl}(biphenyl-4-ylsulfonyl)amino]-3-methylbutanoic acid


Mass: 762.847 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H42N4O12S2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.25
Details: protein solution: 415.2 micro-M MMP9 WT + 0.120 M Acetohydroxamic acid in 20 mM Tris pH 7.0 with 0.001 M inhibitor DC27 and 10% DMSO. precipitant: 40% MPEG 5K ; 0.1 M bicine ; pH 7.25 ...Details: protein solution: 415.2 micro-M MMP9 WT + 0.120 M Acetohydroxamic acid in 20 mM Tris pH 7.0 with 0.001 M inhibitor DC27 and 10% DMSO. precipitant: 40% MPEG 5K ; 0.1 M bicine ; pH 7.25 sitting drops of 1 micro-L protein solution and 1 micro-L precipitant solution. cryoprotectant:_40% cryomix CM2 (25 % di-ethylene glycol + 25 % glycerol + 25 % 1,2-propanediol), 10% PEG 10K, 200 milli-M NaCl, 100 milli-M Na propionate, Na cacodylate, Bis-Tris-propane (PCTP 50% acid/50% basic) pH 7.0 + 0.001 M inhibitor DC27.
PH range: 7-7.25 / Temp details: cooled incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryonozzle
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 19, 2014 / Details: mirrors
RadiationMonochromator: Channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.59→35 Å / Num. obs: 20981 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Biso Wilson estimate: 27.18 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.111 / Net I/σ(I): 15.04
Reflection shellResolution: 1.59→1.63 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.63 / Mean I/σ(I) obs: 1.65 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H3X

4h3x


Resolution: 1.59→34.26 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.47
RfactorNum. reflection% reflection
Rfree0.228 1047 5 %
Rwork0.188 --
obs0.19 20929 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.59→34.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 71 117 1437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061444
X-RAY DIFFRACTIONf_angle_d1.0331974
X-RAY DIFFRACTIONf_dihedral_angle_d15.884504
X-RAY DIFFRACTIONf_chiral_restr0.044195
X-RAY DIFFRACTIONf_plane_restr0.006263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.589-1.67280.37541430.34912717X-RAY DIFFRACTION98
1.6728-1.77760.28181470.28792784X-RAY DIFFRACTION100
1.7776-1.91480.27521470.22412792X-RAY DIFFRACTION100
1.9148-2.10750.23061480.18662818X-RAY DIFFRACTION100
2.1075-2.41230.2181490.17272824X-RAY DIFFRACTION100
2.4123-3.0390.22241520.18612898X-RAY DIFFRACTION100
3.039-34.26790.20941610.16433049X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 19.946 Å / Origin y: -9.1917 Å / Origin z: 14.9787 Å
111213212223313233
T0.1031 Å20.0322 Å20.0054 Å2-0.2978 Å2-0.0349 Å2--0.1831 Å2
L1.8176 °20.404 °20.2226 °2-2.6271 °21.435 °2--4.3467 °2
S-0.0815 Å °-0.0565 Å °0.0166 Å °0.0877 Å °0.2506 Å °-0.0928 Å °0.1737 Å °0.5501 Å °-0.0924 Å °
Refinement TLS groupSelection details: ALL

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