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- PDB-1zp5: Crystal structure of the complex between MMP-8 and a N-hydroxyure... -

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Basic information

Entry
Database: PDB / ID: 1zp5
TitleCrystal structure of the complex between MMP-8 and a N-hydroxyurea inhibitor
ComponentsNeutrophil collagenase
KeywordsHYDROLASE
Function / homology
Function and homology information


neutrophil collagenase / tumor necrosis factor binding / positive regulation of microglial cell activation / positive regulation of neuroinflammatory response / positive regulation of tumor necrosis factor-mediated signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / Collagen degradation / collagen catabolic process / extracellular matrix disassembly ...neutrophil collagenase / tumor necrosis factor binding / positive regulation of microglial cell activation / positive regulation of neuroinflammatory response / positive regulation of tumor necrosis factor-mediated signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / metalloendopeptidase activity / specific granule lumen / positive regulation of tumor necrosis factor production / tertiary granule lumen / peptidase activity / cellular response to lipopolysaccharide / : / endopeptidase activity / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular region / zinc ion binding
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
Chem-2NI / Neutrophil collagenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCampestre, C. / Agamennone, M. / Tortorella, P. / Preziuso, S. / Biasone, A. / Gavuzzo, E. / Pochetti, G. / Mazza, F. / Tschesche, H. / Gallina, C.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: N-Hydroxyurea as zinc binding group in matrix metalloproteinase inhibition: Mode of binding in a complex with MMP-8.
Authors: Campestre, C. / Agamennone, M. / Tortorella, P. / Preziuso, S. / Biasone, A. / Gavuzzo, E. / Pochetti, G. / Mazza, F. / Hiller, O. / Tschesche, H. / Consalvi, V. / Gallina, C.
#1: Journal: Curr.Med.Chem. / Year: 2002
Title: Hydroxamic acids as pharmacological agents.
Authors: Muri, E.M. / Nieto, M.J. / Sindelar, R.D. / Williamson, J.S.
#2: Journal: Biochemistry / Year: 1995
Title: Structure determination and analysis of human neutrophil collagenase complexed with a hydroxamate inhibitor.
Authors: Grams, F. / Crimmin, M. / Hinnes, L. / Huxley, P. / Pieper, M. / Tschesche, H. / Bode, W.
#3: Journal: J.Am.Chem.Soc. / Year: 1997
Title: Discovery of potent non peptide inhibitors of stromelysin using SAR by NMR.
Authors: Hajduck, P.J. / Sheppard, G. / Nettesheim, D.G. / Olejniczak, E.T. / Shuker, S.B. / Meadows, R.P. / Steinman, D.H. / Carrera, G.M. / Marcotte, P.A. / Severin, J. / Walter, K. / Smith, H. / ...Authors: Hajduck, P.J. / Sheppard, G. / Nettesheim, D.G. / Olejniczak, E.T. / Shuker, S.B. / Meadows, R.P. / Steinman, D.H. / Carrera, G.M. / Marcotte, P.A. / Severin, J. / Walter, K. / Smith, H. / Gubbins, E. / Simmer, R. / Holzman, T.F. / Morgan, D.W. / Davidsen, S.K. / Summers, J.B. / Fesik, S.W.
#4: Journal: Bioorg.Med.Chem.Lett. / Year: 2001
Title: Biaryl ether retrohydroxamates as potent, long-lived, orally bioavailable MMP inhibitors.
Authors: Michaelides, M.R. / Dellaria, J.F. / Gong, J. / Holms, J.H. / Bouska, J.J. / Stacey, J. / Wada, C.K. / Heyman, H.R. / Curtin, M.L. / Guo, Y. / Goodfellow, C.L. / Elmore, I.B. / Albert, D.H. ...Authors: Michaelides, M.R. / Dellaria, J.F. / Gong, J. / Holms, J.H. / Bouska, J.J. / Stacey, J. / Wada, C.K. / Heyman, H.R. / Curtin, M.L. / Guo, Y. / Goodfellow, C.L. / Elmore, I.B. / Albert, D.H. / Magoc, T.J. / Marcotte, P.A. / Morgan, D.W. / Davidsen, S.K.
History
DepositionMay 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Aug 23, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neutrophil collagenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6346
Polymers18,1121
Non-polymers5225
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.387, 52.675, 67.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Neutrophil collagenase / Matrix metalloproteinase-8 / MMP-8 / PMNL collagenase / PMNL-CL


Mass: 18111.744 Da / Num. of mol.: 1 / Fragment: Catalytic domain (80-242)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP8, CLG1 / Plasmid: pSVB30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P22894, neutrophil collagenase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-2NI / N-{2-[(4'-CYANO-1,1'-BIPHENYL-4-YL)OXY]ETHYL}-N'-HYDROXY-N-METHYLUREA


Mass: 311.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17N3O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.57 Å3/Da / Density % sol: 20.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG6000, MES/NAOH, Na Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 18, 2004
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 10932 / Num. obs: 10932 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3.48 / % possible all: 95.6

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I76

1i76


Resolution: 1.8→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.251 974 random
Rwork0.216 --
all0.219 9738 -
obs0.219 9738 -
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 27 125 1435
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4

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