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- PDB-7dyx: Human JMJD5 in complex with MN and 5-((2-cyclopropylbenzyl)amino)... -

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Basic information

Entry
Database: PDB / ID: 7dyx
TitleHuman JMJD5 in complex with MN and 5-((2-cyclopropylbenzyl)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-HRR / : / Bifunctional peptidase and arginyl-hydroxylase JMJD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,6293
Polymers27,2621
Non-polymers3672
Water1,02757
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 area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.920, 64.750, 78.649
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-HRR / 5-((2-cyclopropylbenzyl)amino)pyridine-2,4-dicarboxylic acid


Mass: 312.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
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: 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: 2.27→48.92 Å / Num. obs: 21676 / % possible obs: 97.1 % / Redundancy: 2.32 % / Biso Wilson estimate: 38.22 Å2 / CC1/2: 0.943 / Rmerge(I) obs: 0.435 / Net I/σ(I): 2.69
Reflection shellResolution: 2.27→2.41 Å / Rmerge(I) obs: 2.966 / Mean I/σ(I) obs: 0.35 / Num. unique obs: 215 / CC1/2: 0.098 / % possible all: 98.2

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Processing

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

6f4p


Resolution: 2.27→41.54 Å / SU ML: 0.3556 / Cross valid method: FREE R-VALUE / σ(F): 0.97 / Phase error: 29.117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2801 1066 4.92 %
Rwork0.2417 20596 -
obs0.2436 21662 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.82 Å2
Refinement stepCycle: LAST / Resolution: 2.27→41.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 0 57 1968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412106
X-RAY DIFFRACTIONf_angle_d0.58292895
X-RAY DIFFRACTIONf_chiral_restr0.047300
X-RAY DIFFRACTIONf_plane_restr0.0033384
X-RAY DIFFRACTIONf_dihedral_angle_d14.6954776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.370.32441340.33942590X-RAY DIFFRACTION97.95
2.37-2.50.38021360.34722602X-RAY DIFFRACTION98.1
2.5-2.650.33971330.33172592X-RAY DIFFRACTION97.6
2.65-2.860.32511350.31122541X-RAY DIFFRACTION96.5
2.86-3.150.33081280.28162502X-RAY DIFFRACTION93.93
3.15-3.60.23251380.22982611X-RAY DIFFRACTION98.35
3.6-4.540.2551300.17332617X-RAY DIFFRACTION98.21
4.54-41.540.25031320.20622541X-RAY DIFFRACTION95.81
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)
13.30001099436-0.7612038799661.643644282322.95612548808-1.588495319912.06642998091-0.379420861668-0.2296396200430.3692847694210.244229582910.1627429762230.119619241035-0.265230553572-0.2524981559130.09293327190110.2689090828320.003197824143430.0487416507180.261658605056-0.03171864948190.325582787887-13.114825538714.8208971611-15.0764346809
21.100428169760.3018570096870.4631410516071.75791596289-0.8909837037352.63156991286-0.004702954682630.025440425663-0.08387057754980.0271286517774-0.01428606085530.07333664311140.107353057201-0.007011852656220.01788835724250.2153307229270.02798071701480.03478175558390.19476818306-0.02934188241520.364455189865-8.0712655655512.9960925544-23.0646073939
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 182 through 248 )
2X-RAY DIFFRACTION2chain 'A' and (resid 249 through 416 )

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