[English] 日本語
Yorodumi
- PDB-5h8x: Crystal structure of the complex MMP-8/BF471 (catechol inhibitor) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5h8x
TitleCrystal structure of the complex MMP-8/BF471 (catechol inhibitor)
ComponentsNeutrophil collagenase
KeywordsHYDROLASE / Catechol function / MMPs / inhibitor / metalloprotese / zinc binding function
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 / collagen-containing extracellular matrix / endopeptidase activity / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / zinc ion binding / extracellular region
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-5XT / Chem-7FY / Neutrophil collagenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsPochetti, G. / Montanari, R. / Capelli, D. / Tortorella, P.
CitationJournal: J Enzyme Inhib Med Chem / Year: 2016
Title: Catechol-based matrix metalloproteinase inhibitors with additional antioxidative activity.
Authors: Tauro, M. / Laghezza, A. / Loiodice, F. / Piemontese, L. / Caradonna, A. / Capelli, D. / Montanari, R. / Pochetti, G. / Di Pizio, A. / Agamennone, M. / Campestre, C. / Tortorella, P.
History
DepositionDec 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Jan 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 / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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)19,2018
Polymers18,1121
Non-polymers1,0897
Water2,900161
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-6 kcal/mol
Surface area7870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.910, 68.460, 68.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 18111.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP8, CLG1 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22894, neutrophil collagenase

-
Non-polymers , 6 types, 168 molecules

#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-5XT / ~{N}-[3,4-bis(oxidanyl)phenyl]-4-phenyl-benzenesulfonamide


Mass: 341.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15NO4S
#5: Chemical ChemComp-7FY / ~{N}-[4,5-bis(oxidanylidene)cyclohexen-1-yl]-4-phenyl-benzenesulfonamide


Mass: 341.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15NO4S
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.29 % / Description: thin needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10 % PEG 6000, 0.2M MES/NAOH, 1M NA REMARK 280 PHOSPHATE, PH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2013
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.3→29.67 Å / Num. obs: 38061 / % possible obs: 98.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.8
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 2 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
iMOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DPE

3dpe


Resolution: 1.3→29.666 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 20.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 2006 5.28 %Random selection
Rwork0.1951 ---
obs0.1962 37993 97.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→29.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 64 161 1508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071385
X-RAY DIFFRACTIONf_angle_d1.2311892
X-RAY DIFFRACTIONf_dihedral_angle_d19.221501
X-RAY DIFFRACTIONf_chiral_restr0.055184
X-RAY DIFFRACTIONf_plane_restr0.007251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.33250.32471420.30142534X-RAY DIFFRACTION97
1.3325-1.36850.28311390.27652559X-RAY DIFFRACTION98
1.3685-1.40880.28091450.24382542X-RAY DIFFRACTION99
1.4088-1.45430.2361410.22852538X-RAY DIFFRACTION98
1.4543-1.50620.20961420.2112570X-RAY DIFFRACTION98
1.5062-1.56650.21051420.19262540X-RAY DIFFRACTION98
1.5665-1.63780.21371390.18662526X-RAY DIFFRACTION97
1.6378-1.72420.21591460.16942582X-RAY DIFFRACTION99
1.7242-1.83220.20141440.16462586X-RAY DIFFRACTION99
1.8322-1.97360.18761420.17122550X-RAY DIFFRACTION98
1.9736-2.17220.18261440.16152545X-RAY DIFFRACTION96
2.1722-2.48630.19621420.18222578X-RAY DIFFRACTION97
2.4863-3.1320.22021490.19632680X-RAY DIFFRACTION99
3.132-29.67420.22451490.19992657X-RAY DIFFRACTION94

+
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://pdbjlvh1.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