[English] 日本語
Yorodumi
- PDB-4wx4: Crystal structure of adenovirus 8 protease in complex with a nitr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wx4
TitleCrystal structure of adenovirus 8 protease in complex with a nitrile inhibitor
Components
  • Protease
  • peptide
KeywordsHYDROLASE / cysteine protease / inhibitor / cofactor
Function / homology
Function and homology information


adenain / virion component / cysteine-type endopeptidase activity / host cell nucleus / proteolysis / DNA binding
Similarity search - Function
Peptidase C5, adenain / Adenovirus endoprotease / Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Papain-like cysteine peptidase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3VF / GLYCINE / Protease
Similarity search - Component
Biological speciesHuman adenovirus D serotype 8
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.03 Å
AuthorsGrosche, P. / Sirockin, F. / Mac Sweeney, A. / Ramage, P. / Erbel, P. / Melkko, S. / Bernardi, A. / Hughes, N. / Ellis, D. / Combrink, K. ...Grosche, P. / Sirockin, F. / Mac Sweeney, A. / Ramage, P. / Erbel, P. / Melkko, S. / Bernardi, A. / Hughes, N. / Ellis, D. / Combrink, K. / Jarousse, N. / Altmann, E.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Structure-based design and optimization of potent inhibitors of the adenoviral protease.
Authors: Grosche, P. / Sirockin, F. / Mac Sweeney, A. / Ramage, P. / Erbel, P. / Melkko, S. / Bernardi, A. / Hughes, N. / Ellis, D. / Combrink, K.D. / Jarousse, N. / Altmann, E.
History
DepositionNov 13, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protease
C: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2355
Polymers24,4382
Non-polymers7973
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint2 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.454, 42.790, 59.059
Angle α, β, γ (deg.)90.000, 93.160, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein Protease


Mass: 23124.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus D serotype 8 / References: UniProt: B9A5C1
#2: Protein/peptide peptide


Mass: 1313.639 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 253 molecules

#3: Chemical ChemComp-3VF / N-[(2-cyanopyrimidin-4-yl)methyl]-3-[2-(3,5-dichlorophenyl)-2-methylpropanoyl]-4-methoxybenzamide


Mass: 483.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H20Cl2N4O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Crystallization Reservoir Solution = 0.2M proline, 0.1M HEPES pH 7.5, 10% PEG3350 Crystallization Protein Solution = 5 mg/ml adenain in 20 mM Tris, 100 mM NaCl, pH 7.6. 5 mM inhibitor added.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.03→58.9 Å / Num. obs: 102036 / % possible obs: 85.7 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 11.29 Å2 / Rmerge F obs: 0.029 / Rmerge(I) obs: 0.025 / Rrim(I) all: 0.029 / Χ2: 1.015 / Net I/σ(I): 26.93 / Num. measured all: 273190
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.03-1.061.60.1370.0836.274815753529960.1139.8
1.06-1.090.1030.078.57427728939510.08954.2
1.09-1.120.0880.06511.311827712850130.08270.3
1.12-1.150.0680.0615.0119103694360960.07287.8
1.15-1.190.0580.05617.1820470671860860.06790.6
1.19-1.230.0550.05218.2318929645958920.06291.2
1.23-1.280.0480.04920.3719155625957790.05892.3
1.28-1.330.0420.04322.7119134603356300.05193.3
1.33-1.390.0390.0424.417904579854500.04894
1.39-1.460.0350.03726.3416846552552350.04594.8
1.46-1.540.0280.03330.9217368528350580.03995.7
1.54-1.630.0250.0334.1516253498048120.03596.6
1.63-1.740.0230.02735.8314317470945290.03396.2
1.74-1.880.0210.02539.8714340435342260.0397.1
1.88-2.060.0180.02343.7213480404539460.02897.6
2.06-2.30.0170.02345.3211747365535680.02797.6
2.3-2.660.0170.02245.719974322931470.02697.5
2.66-3.260.0150.02149.189287274726980.02598.2
3.26-4.610.0150.0248.726746214021130.02598.7
4.610.0150.02150.524068121011860.02698

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 1.03→34.79 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.3082 / WRfactor Rwork: 0.2413 / FOM work R set: 0.705 / SU B: 0.482 / SU ML: 0.012 / SU Rfree: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.023 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1365 4371 5 %RANDOM
Rwork0.1172 83041 --
obs0.1182 83041 85.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.37 Å2 / Biso mean: 12.065 Å2 / Biso min: 4.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.1 Å2
2--0 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.03→34.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1587 0 48 250 1885
Biso mean--8.8 22.68 -
Num. residues----212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0191857
X-RAY DIFFRACTIONr_angle_refined_deg2.1941.982524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2985230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.20620.90988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03915307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1241524
X-RAY DIFFRACTIONr_chiral_restr0.160.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211459
X-RAY DIFFRACTIONr_rigid_bond_restr10.66631857
X-RAY DIFFRACTIONr_sphericity_free29.022544
X-RAY DIFFRACTIONr_sphericity_bonded13.76152002
LS refinement shellResolution: 1.03→1.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.157 148 -
Rwork0.128 2809 -
all-2957 -
obs--39.44 %

+
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