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- PDB-1utt: Crystal Structure of MMP-12 complexed to 2-(1,3-dioxo-1,3-dihydro... -

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Basic information

Entry
Database: PDB / ID: 1utt
TitleCrystal Structure of MMP-12 complexed to 2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)ethyl-4-(4-ethoxy[1,1-biphenyl]-4-yl)-4-oxobutanoic acid
ComponentsMACROPHAGE METALLOELASTASE
KeywordsHYDROLASE / MACROPHAGE METALLOELASTASE / NON-ZINC CHELATOR / MMP-12 / MMP INHIBITOR / METALLOPROTEASE
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-CP8 / ACETOHYDROXAMIC ACID / Macrophage metalloelastase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMorales, R. / Perrier, S. / Florent, J.M. / Beltra, J. / Dufour, S. / De Mendez, I. / Manceau, P. / Tertre, A. / Moreau, F. / Compere, D. ...Morales, R. / Perrier, S. / Florent, J.M. / Beltra, J. / Dufour, S. / De Mendez, I. / Manceau, P. / Tertre, A. / Moreau, F. / Compere, D. / Dublanchet, A.C. / O'Gara, M.
CitationJournal: J. Mol. Biol. / Year: 2004
Title: Crystal structures of novel non-peptidic, non-zinc chelating inhibitors bound to MMP-12.
Authors: Morales, R. / Perrier, S. / Florent, J.M. / Beltra, J. / Dufour, S. / De Mendez, I. / Manceau, P. / Tertre, A. / Moreau, F. / Compere, D. / Dublanchet, A.C. / O'Gara, M.
History
DepositionDec 10, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 27, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_label_seq_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: MACROPHAGE METALLOELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3709
Polymers17,6321
Non-polymers7398
Water1,74797
1
A: MACROPHAGE METALLOELASTASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)110,22254
Polymers105,7906
Non-polymers4,43248
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_646-y+1,z-1/2,-x+3/21
crystal symmetry operation7_665-z+3/2,-x+1,y+1/21
crystal symmetry operation13_546y+3/4,x-3/4,-z+5/41
crystal symmetry operation19_655-x+7/4,-z+3/4,-y+3/41
crystal symmetry operation22_554z+1/4,-y+1/4,x-1/41
MethodPQS
Unit cell
Length a, b, c (Å)125.041, 125.041, 125.041
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-1272-

CA

DetailsOUR DYNAMIC LIGHT SCATTERING EXPERIMENTS HAVE SHOWN THATTHE PROTEIN EXISTS AS A MONOMER IN SOLUTION, SUGGESTINGTHAT THE HEXAMER DESCRIBED IN REMARK 350 IS AN ARTIFACTOF CRYSTALLIZATION ONLY. THE PROTEIN IS KNOWN TO FUNCTIONAS A MONOMER

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Components

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Protein , 1 types, 1 molecules A

#1: Protein MACROPHAGE METALLOELASTASE / HME / MATRIX METALLOPROTEINASE-12 / MMP-12 / MACROPHAGE ELASTASE / ME


Mass: 17631.648 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 106-264
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH A SMALL MOLECULE INHIBITOR 2-(1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL)ETHYL-4-(4-ETHOXY[1,1-BIPHENYL]-4-YL)-4-OXOBUTANOIC ACID FORMULA C19H19N2O4S, AND ALSO WITH ...Details: COMPLEXED WITH A SMALL MOLECULE INHIBITOR 2-(1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL)ETHYL-4-(4-ETHOXY[1,1-BIPHENYL]-4-YL)-4-OXOBUTANOIC ACID FORMULA C19H19N2O4S, AND ALSO WITH ACETOHYDROXAMIC ACID OR 2-HYDROXYAMINO-2-ETHANAL FORMULA, C2H5NO2
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEMEX1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39900, macrophage elastase

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Non-polymers , 5 types, 105 molecules

#2: Chemical ChemComp-HAE / ACETOHYDROXAMIC ACID


Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2 / Comment: inhibitor, medication*YM
#3: Chemical ChemComp-CP8 / 2-(1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL) ETHYL-4-(4'-ETHOXY [1,1'-BIPHENYL]-4-YL)-4-OXOBUTANOIC ACID / CP-271485 / (6R)-4-BENZYL-6-(1-METHYL-2,2-DIOXIDO-1,3-DIHYDRO-2,1-BENZISOTHIAZOL-5-YL)MORPHOLIN-3-ONE


Mass: 372.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20N2O4S
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsMAY BE INVOLVED IN TISSUE INJURY AND REMODELING. HAS SIGNIFICANT ELASTOLYTIC ACTIVITY. BINDS 2 ZINC ...MAY BE INVOLVED IN TISSUE INJURY AND REMODELING. HAS SIGNIFICANT ELASTOLYTIC ACTIVITY. BINDS 2 ZINC IONS AND 4 CALCIUM IONS PER SUBUNIT. FOUND IN ALVEOLAR MACROPHAGES BUT NOT IN PERIPHERAL BLOOD MONOCYTES.

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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: 4.2 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M SODIUM CACODYLATE PH 6.4, 1.4M AMMONIUM ACETATE, 4 C

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU-MSC RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 15, 2002 / Details: RIGAKU-MSC OSMIC MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 17420 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6.98 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 25.63
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 24 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 4.74 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNX2001refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JK3
Resolution: 2.2→30 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 840 5 %RANDOM
Rwork0.217 ---
obs-17406 90.2 %-
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 37 97 1383
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005735
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.17
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.25 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.3105 51 -
Rwork0.2386 896 -
obs--98 %

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