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- PDB-7dyt: Human JMJD5 in complex with MN and 5-((4-methoxybenzyl)amino)pyri... -

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Basic information

Entry
Database: PDB / ID: 7dyt
TitleHuman JMJD5 in complex with MN and 5-((4-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 / regulation of signal transduction by p53 class mediator / circadian regulation of gene expression / protein destabilization / G2/M transition of mitotic cell cycle ...[protein]-arginine 3-hydroxylase / peptidyl-arginine 3-dioxygenase activity / histone H3K36 demethylase activity / Hydrolases; Acting on peptide bonds (peptidases) / Protein hydroxylation / aminopeptidase activity / 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
: / KDM8-like, N-terminal ARM repeats / 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-HR3 / : / Bifunctional peptidase and arginyl-hydroxylase JMJD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,6193
Polymers27,2621
Non-polymers3572
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-6 kcal/mol
Surface area11260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.350, 65.000, 78.610
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

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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: 27261.873 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-HR3 / 5-((4-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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.81 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.62→50.09 Å / Num. obs: 30389 / % possible obs: 92.5 % / Redundancy: 10.3 % / Biso Wilson estimate: 21.58 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.161 / Net I/σ(I): 11.2
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.117 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 965 / CC1/2: 0.451 / % possible all: 59.2

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Processing

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

6f4p


Resolution: 1.62→41.8 Å / SU ML: 0.2129 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.706
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.189 1502 4.95 %
Rwork0.1625 28833 -
obs0.1638 30335 92.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.98 Å2
Refinement stepCycle: LAST / Resolution: 1.62→41.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 22 228 2134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00482179
X-RAY DIFFRACTIONf_angle_d0.7633000
X-RAY DIFFRACTIONf_chiral_restr0.0504307
X-RAY DIFFRACTIONf_plane_restr0.0054403
X-RAY DIFFRACTIONf_dihedral_angle_d15.2598816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.670.4077830.36651742X-RAY DIFFRACTION61.99
1.67-1.730.3667960.3362054X-RAY DIFFRACTION73.71
1.73-1.80.32441210.27912379X-RAY DIFFRACTION85.09
1.8-1.880.23711360.21642667X-RAY DIFFRACTION95.18
1.88-1.980.21881400.1722799X-RAY DIFFRACTION98.99
1.98-2.110.19871470.16422811X-RAY DIFFRACTION99.9
2.11-2.270.17231460.14662829X-RAY DIFFRACTION99.97
2.27-2.50.18221650.14062814X-RAY DIFFRACTION100
2.5-2.860.17571680.14922812X-RAY DIFFRACTION99.93
2.86-3.60.17971520.14222896X-RAY DIFFRACTION99.97
3.6-41.80.16011480.15183030X-RAY DIFFRACTION99.97
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)
12.55251428547-1.426360936520.5467946888332.02051851983-0.6925314428411.54105086892-0.145730744682-0.1667555535680.07136142813030.2321215837160.2161066350120.158242778454-0.218496007217-0.264637629895-0.009412171944760.1643893967210.01235548663340.05708841679790.152206693096-0.002461230076910.15507451993-18.517810387417.4123052535-13.523132363
23.059864088290.813254636271-2.630351829484.10948066885-2.354181962814.551958118360.01692214061430.394908707930.0405211610625-0.327298234623-0.0605755167033-0.2149569483640.1040846002740.05792230671090.02823933938890.1804527125490.03397500094370.02068101073160.2000313375710.01304755603830.1888132115434.28757901173.5866062465-16.6062773599
31.40766643250.0596737256233-0.3872632781271.38934972489-0.6465702576921.74583640924-0.01542275518460.0346953498921-0.141026944791-0.02216033540690.0286114198189-0.01963152720650.035796324568-0.0829167939211-0.02269165632360.106157319282-0.002259449479370.001412758926320.0801537856281-0.01922888053430.11534782176-9.4008274069613.9666179203-23.8833695993
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 182 through 230 )
2X-RAY DIFFRACTION2chain 'A' and (resid 231 through 262 )
3X-RAY DIFFRACTION3chain 'A' and (resid 263 through 416 )

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