[English] 日本語
Yorodumi
- PDB-7dyw: Human JMJD5 in complex with MN and 5-((2-methoxybenzyl)amino)pyri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dyw
TitleHuman JMJD5 in complex with MN and 5-((2-methoxybenzyl)amino)pyridine-2,4-dicarboxylic acid.
ComponentsBifunctional peptidase and arginyl-hydroxylase JMJD5
KeywordsOXIDOREDUCTASE / JmjC domain-containing protein 5 / JMJD5 / dioxygenase
Function / homology
Function and homology information


[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / methylated histone binding / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization ...[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / methylated histone binding / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization / G2/M transition of mitotic cell cycle / p53 binding / chromosome / fibroblast proliferation / endopeptidase activity / in utero embryonic development / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of DNA-templated transcription / proteolysis / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
Cupin-like domain 8 / Cupin-like domain / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile.
Similarity search - Domain/homology
Chem-HRL / : / Bifunctional peptidase and arginyl-hydroxylase JMJD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsNakashima, Y. / Brewitz, L. / Schofield, C.J.
CitationJournal: J.Med.Chem. / Year: 2023
Title: 5-Substituted Pyridine-2,4-dicarboxylate Derivatives Have Potential for Selective Inhibition of Human Jumonji-C Domain-Containing Protein 5.
Authors: Brewitz, L. / Nakashima, Y. / Piasecka, S.K. / Salah, E. / Fletcher, S.C. / Tumber, A. / Corner, T.P. / Kennedy, T.J. / Fiorini, G. / Thalhammer, A. / Christensen, K.E. / Coleman, M.L. / Schofield, C.J.
History
DepositionJan 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Dec 6, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bifunctional peptidase and arginyl-hydroxylase JMJD5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7473
Polymers27,3901
Non-polymers3572
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-6 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.642, 65.415, 79.566
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Bifunctional peptidase and arginyl-hydroxylase JMJD5 / JmjC domain-containing protein 5 / Jumonji C domain-containing protein 5 / L-arginine (3R)-hydroxylase KDM8


Mass: 27390.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM8, JMJD5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8N371, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen ...References: UniProt: Q8N371, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-HRL / 5-((2-methoxybenzyl)amino)pyridine-2,4-dicarboxylic acid


Mass: 302.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM HEPES sodium, 200mM magnesium chloride hexahydrate, 25% w/v PEG 3350, 1mM manganese chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 2.13→42.12 Å / Num. obs: 27195 / % possible obs: 97.3 % / Redundancy: 2.81 % / Biso Wilson estimate: 42.4 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.202 / Net I/σ(I): 6
Reflection shellResolution: 2.13→2.26 Å / Rmerge(I) obs: 2.864 / Mean I/σ(I) obs: 0.43 / Num. unique obs: 1249 / CC1/2: 0.129 / % possible all: 92.6

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F4P

6f4p


Resolution: 2.13→42.12 Å / SU ML: 0.3191 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 26.5194
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2392 1346 4.96 %
Rwork0.2142 25781 -
obs0.2154 27127 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.09 Å2
Refinement stepCycle: LAST / Resolution: 2.13→42.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 22 72 2022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01192162
X-RAY DIFFRACTIONf_angle_d0.94042974
X-RAY DIFFRACTIONf_chiral_restr0.0543306
X-RAY DIFFRACTIONf_plane_restr0.0063397
X-RAY DIFFRACTIONf_dihedral_angle_d14.4293802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.210.37541270.37422401X-RAY DIFFRACTION91.26
2.21-2.30.32441360.32752615X-RAY DIFFRACTION98.78
2.3-2.40.32471400.32962626X-RAY DIFFRACTION98.96
2.4-2.530.3411390.30852603X-RAY DIFFRACTION98.85
2.53-2.690.34361380.29012598X-RAY DIFFRACTION98.56
2.69-2.90.30931350.25612584X-RAY DIFFRACTION98.12
2.9-3.190.22261310.2212601X-RAY DIFFRACTION97.5
3.19-3.650.24491300.18032590X-RAY DIFFRACTION98.27
3.65-4.590.15791340.14292591X-RAY DIFFRACTION97.71
4.6-42.120.20791360.19192572X-RAY DIFFRACTION97.41
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.691184786540.278032608271-4.264682797052.078817593570.04631681452462.76893534453-0.4253995362350.34342576571-0.409860210043-0.453426715868-0.17469652711-0.2525067352030.2460792016540.6721366357830.6423308336710.4520543669890.0166755868021-0.01690793530650.460406495917-0.03387484650860.4893819347475.415720828432.9652179158-14.7591346659
21.845159561-0.7104397153160.8531734174452.78921038871-0.6732116741922.433172019710.0817125187067-0.0702414102663-0.3316552138620.268855587108-0.04643738765330.06808163070220.127465448133-0.037364090098-0.009465197893940.36515593471-0.001638336025190.002106555966740.328560032050.006594435088340.365387375427-10.05879025397.71033429731-17.3016658673
32.577417364410.459790122697-1.089619249982.09072419269-1.619032104664.058551855650.02757390430260.128679572208-0.127244944959-0.007975122537670.0111268052767-0.00275776465381-0.00684163861093-0.00743227115023-0.006769594922110.3006353510050.0204338577084-0.009978761503660.283134142311-0.03707573248780.358174038838-9.0604362880518.0079077436-28.8831459718
46.999655860731.517195812630.05632650825964.058257753041.832901993714.61685872798-0.199660809093-0.1618511135350.527206018320.07636457935520.02254236722070.926036870626-0.68833090283-1.192618466860.1122762167040.3278973419480.146484684169-0.02018101504280.46135438463-0.001871494474650.483058705131-25.787496574922.4450798409-21.6066764258
52.14114725771-1.05058256091.581422693942.71885384274-0.568941881161.29706567144-0.261980598469-0.05214666129110.2326557315870.2352635962960.271634123885-0.402714158675-0.1038521130320.203090553346-0.03061922542510.479403938359-0.0348829640855-0.01276137599180.420266828861-0.02054514951650.424224754212-4.5510025652610.1510018711-12.7611865964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 249 through 262 )
2X-RAY DIFFRACTION2chain 'A' and (resid 263 through 325 )
3X-RAY DIFFRACTION3chain 'A' and (resid 326 through 416 )
4X-RAY DIFFRACTION4chain 'A' and (resid 182 through 205 )
5X-RAY DIFFRACTION5chain 'A' and (resid 206 through 248 )

+
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