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- PDB-5f5c: Crystal Structure of human JMJD2D complexed with KDOPP7 -

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Basic information

Entry
Database: PDB / ID: 5f5c
TitleCrystal Structure of human JMJD2D complexed with KDOPP7
ComponentsLysine-specific demethylase 4D
KeywordsOXIDOREDUCTASE / DOUBLE-STRANDED BETA HELIX / DEMETHYLASE / OXYGENASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation ...positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation / HDMs demethylate histones / chromatin DNA binding / site of double-strand break / regulation of gene expression / blood microparticle / damaged DNA binding / chromatin remodeling / inflammatory response / chromatin / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls ...JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-5V3 / NICKEL (II) ION / Lysine-specific demethylase 4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsKrojer, T. / Vollmar, M. / Crawley, L. / Bradley, A.R. / Szykowska, A. / Ruda, G.F. / Yang, H. / Burgess-Brown, N. / Brennan, P. / Bountra, C. ...Krojer, T. / Vollmar, M. / Crawley, L. / Bradley, A.R. / Szykowska, A. / Ruda, G.F. / Yang, H. / Burgess-Brown, N. / Brennan, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Oppermann, U. / von Delft, F. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2016
Title: 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.
Authors: Bavetsias, V. / Lanigan, R.M. / Ruda, G.F. / Atrash, B. / McLaughlin, M.G. / Tumber, A. / Mok, N.Y. / Le Bihan, Y.V. / Dempster, S. / Boxall, K.J. / Jeganathan, F. / Hatch, S.B. / Savitsky, ...Authors: Bavetsias, V. / Lanigan, R.M. / Ruda, G.F. / Atrash, B. / McLaughlin, M.G. / Tumber, A. / Mok, N.Y. / Le Bihan, Y.V. / Dempster, S. / Boxall, K.J. / Jeganathan, F. / Hatch, S.B. / Savitsky, P. / Velupillai, S. / Krojer, T. / England, K.S. / Sejberg, J. / Thai, C. / Donovan, A. / Pal, A. / Scozzafava, G. / Bennett, J.M. / Kawamura, A. / Johansson, C. / Szykowska, A. / Gileadi, C. / Burgess-Brown, N.A. / von Delft, F. / Oppermann, U. / Walters, Z. / Shipley, J. / Raynaud, F.I. / Westaway, S.M. / Prinjha, R.K. / Fedorov, O. / Burke, R. / Schofield, C.J. / Westwood, I.M. / Bountra, C. / Muller, S. / van Montfort, R.L. / Brennan, P.E. / Blagg, J.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Structure summary
Revision 1.3Jan 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific demethylase 4D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,00612
Polymers40,0171
Non-polymers98911
Water7,404411
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-27 kcal/mol
Surface area14810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.594, 71.594, 150.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-812-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysine-specific demethylase 4D / JmjC domain-containing histone demethylation protein 3D / Jumonji domain-containing protein 2D


Mass: 40017.348 Da / Num. of mol.: 1 / Fragment: Oxidoreductase-2OG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4D, JHDM3D, JMJD2D / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6B0I6, 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

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Non-polymers , 6 types, 422 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-5V3 / 8-[[(phenylmethyl)amino]methyl]-1~{H}-pyrido[3,4-d]pyrimidin-4-one


Mass: 266.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14N4O
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 26% PEG3350 , 0.1M HEPES pH 6.8 , 0.2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.88→64.68 Å / Num. all: 32698 / Num. obs: 32698 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 13.5
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 3.95 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 1.96 / % possible all: 97.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SADABSdata scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
SAINTdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4d6q

4d6q


Resolution: 1.88→51.92 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.898 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 1635 5 %RANDOM
Rwork0.1715 ---
obs0.1734 30964 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.85 Å2 / Biso mean: 13.863 Å2 / Biso min: 2.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.88→51.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2665 0 57 411 3133
Biso mean--29.99 26.42 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192991
X-RAY DIFFRACTIONr_bond_other_d0.0020.022714
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.9464076
X-RAY DIFFRACTIONr_angle_other_deg1.00236255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2255371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22223.691149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10715483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9921519
X-RAY DIFFRACTIONr_chiral_restr0.1060.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213518
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02765
X-RAY DIFFRACTIONr_mcbond_it0.5720.7551424
X-RAY DIFFRACTIONr_mcbond_other0.5720.7541423
X-RAY DIFFRACTIONr_mcangle_it11.1281815
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 120 -
Rwork0.268 2182 -
all-2302 -
obs--97.54 %
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)
10.49170.02780.46160.33520.14850.9689-0.01740.03720.0553-0.01420.01760.0245-0.1074-0.0859-0.00020.0390.02740.00030.04150.00860.0483-5.38747.310816.8998
20.6575-0.06880.03820.62680.3480.94190.0060.00470.0085-0.00410.0078-0.0809-0.02410.1503-0.01380.0166-0.00840.00880.04230.02150.044722.71910.955317.8928
32.201-0.1248-0.76540.28470.25980.60260.0642-0.05940.04290.0545-0.0491-0.0339-0.03470.02-0.01520.0792-0.0074-0.01210.03370.0090.009110.45624.388628.4983
40.45530.2404-0.0940.24240.08170.20930.067-0.0028-0.00120.0614-0.0547-0.02780.0097-0.0286-0.01230.0666-0.01410.00130.04870.02320.02662.441-4.377327.0149
50.3979-0.1705-0.17680.28130.15410.2599-0.0073-0.0103-0.0179-0.0083-0.0220.01250.00080.01430.02920.05290.00440.0010.04330.02010.03727.2219-6.377513.2232
64.6441-1.1638-1.60541.70540.05990.6391-0.0472-0.1811-0.21140.0402-0.00480.17020.01560.07650.05190.0335-0.00590.01610.03970.01140.0338-1.37-15.891822.2984
73.4671-0.616-0.24833.32452.15212.3206-0.22420.1186-0.17430.32550.11370.0268-0.01290.24430.11050.0919-0.032-0.01030.04350.01670.0252-0.2819-21.885729.0998
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 62
2X-RAY DIFFRACTION2A63 - 131
3X-RAY DIFFRACTION3A132 - 151
4X-RAY DIFFRACTION4A152 - 194
5X-RAY DIFFRACTION5A195 - 297
6X-RAY DIFFRACTION6A298 - 318
7X-RAY DIFFRACTION7A319 - 340

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