[English] 日本語
Yorodumi
- PDB-1zp5: Crystal structure of the complex between MMP-8 and a N-hydroxyure... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more