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- PDB-1utz: Crystal Structure of MMP-12 complexed to (2R)-3-({[4-[(pyridin-4-... -

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Basic information

Entry
Database: PDB / ID: 1utz
TitleCrystal Structure of MMP-12 complexed to (2R)-3-({[4-[(pyridin-4-yl)phenyl]-thien-2-yl}carboxamido)(phenyl)propanoic 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 / 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 / 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 / positive regulation of interferon-alpha production / extracellular matrix disassembly / core promoter sequence-specific DNA binding / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / cellular response to virus / 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 / extracellular region / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain ...Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain / 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
ACETOHYDROXAMIC ACID / Chem-PF3 / Macrophage metalloelastase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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 12, 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 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _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.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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MACROPHAGE METALLOELASTASE
B: MACROPHAGE METALLOELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,12115
Polymers35,2632
Non-polymers1,85813
Water2,360131
1
A: MACROPHAGE METALLOELASTASE
B: MACROPHAGE METALLOELASTASE
hetero molecules

A: MACROPHAGE METALLOELASTASE
B: MACROPHAGE METALLOELASTASE
hetero molecules

A: MACROPHAGE METALLOELASTASE
B: MACROPHAGE METALLOELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,36345
Polymers105,7906
Non-polymers5,57339
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)123.224, 123.224, 168.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
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, 2 molecules AB

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


Mass: 17631.648 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 106-264
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH A SMALL MOLECULE INHIBITOR (2R)-3-({[4-[(PYRIDIN-4-YL)PHENYL]-THIEN-2-YL} CARBOXAMIDO)(PHENYL)PROPANOIC ACID FORMULA C25 H19 N2 O2 S AND ALSO WITH ACETOHYDROXAMIC ACID OR 2- ...Details: COMPLEXED WITH A SMALL MOLECULE INHIBITOR (2R)-3-({[4-[(PYRIDIN-4-YL)PHENYL]-THIEN-2-YL} CARBOXAMIDO)(PHENYL)PROPANOIC ACID FORMULA C25 H19 N2 O2 S 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, 144 molecules

#2: Chemical ChemComp-PF3 / (2R)-3-({[4-[(PYRIDIN-4-YL)PHENYL]-THIEN-2-YL}CARBOXAMIDO)(PHENYL)PROPANOIC ACID / PF-00356231 / 3-PHENYL-3-({[4-(4-PYRIDIN-4-YLPHENYL)THIEN-2-YL]CARBONYL}AMINO)PROPANOIC ACID


Mass: 428.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H20N2O3S
#3: Chemical ChemComp-HAE / ACETOHYDROXAMIC ACID


Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2 / Comment: medication*YM
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / 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.: 131 / 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.

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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: 3.37 Å3/Da / Density % sol: 63.54 %
Crystal growTemperature: 293 K / pH: 8 / Details: 0.1M IMIDAZOLE PH 8.0, 2.0-2.5M NACL, 20 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: 2.5→99 Å / Num. obs: 26781 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.98 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 13.22
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 6.46 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 4.1 / % 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

1jk3


Resolution: 2.5→30 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2646 10 %RANDOM
Rwork0.224 ---
obs-17406 99.6 %-
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 111 131 2740
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006836
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_deg1.23112
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: 2.5→2.52 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3151 45 -
Rwork0.2881 493 -
obs--99.8 %

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