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- PDB-5iwg: HDAC2 WITH LIGAND BRD4884 -

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Basic information

Entry
Database: PDB / ID: 5iwg
TitleHDAC2 WITH LIGAND BRD4884
ComponentsHistone deacetylase 2
KeywordsHYDROLASE / HDAC HISTONE DEACETYLASE
Function / homology
Function and homology information


protein de-2-hydroxyisobutyrylase activity / protein lysine delactylase activity / p75NTR negatively regulates cell cycle via SC1 / fungiform papilla formation / epidermal cell differentiation / eyelid development in camera-type eye / protein decrotonylase activity / histone decrotonylase activity / NuRD complex / regulation of cell fate specification ...protein de-2-hydroxyisobutyrylase activity / protein lysine delactylase activity / p75NTR negatively regulates cell cycle via SC1 / fungiform papilla formation / epidermal cell differentiation / eyelid development in camera-type eye / protein decrotonylase activity / histone decrotonylase activity / NuRD complex / regulation of cell fate specification / EGR2 and SOX10-mediated initiation of Schwann cell myelination / negative regulation of stem cell population maintenance / regulation of stem cell differentiation / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / ESC/E(Z) complex / positive regulation of intracellular estrogen receptor signaling pathway / odontogenesis of dentin-containing tooth / STAT3 nuclear events downstream of ALK signaling / embryonic digit morphogenesis / histone deacetylase activity / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Notch-HLH transcription pathway / histone deacetylase complex / positive regulation of stem cell population maintenance / dendrite development / Sin3-type complex / positive regulation of proteolysis / progesterone receptor signaling pathway / RNA Polymerase I Transcription Initiation / hair follicle placode formation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Regulation of MECP2 expression and activity / NF-kappaB binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Regulation of TP53 Activity through Acetylation / MECP2 regulates neuronal receptors and channels / Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells) / negative regulation of cell migration / regulation of embryonic development / transcription repressor complex / negative regulation of transforming growth factor beta receptor signaling pathway / Regulation of PTEN gene transcription / transcription coregulator binding / SUMOylation of chromatin organization proteins / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / circadian regulation of gene expression / negative regulation of neuron projection development / NuRD complex assembly / Regulation of endogenous retroelements by KRAB-ZFP proteins / Interaction of NuRD complexes with transcription factors / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / histone binding / Factors involved in megakaryocyte development and platelet production / heterochromatin formation / Potential therapeutics for SARS / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Histone deacetylase / Histone deacetylase domain / Arginase; Chain A / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-IWX / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / TRIETHYLENE GLYCOL / Histone deacetylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsSteinbacher, S.
CitationJournal: Bioorg.Med.Chem. / Year: 2016
Title: Kinetic and structural insights into the binding of histone deacetylase 1 and 2 (HDAC1, 2) inhibitors.
Authors: Wagner, F.F. / Weiwer, M. / Steinbacher, S. / Schomburg, A. / Reinemer, P. / Gale, J.P. / Campbell, A.J. / Fisher, S.L. / Zhao, W.N. / Reis, S.A. / Hennig, K.M. / Thomas, M. / Muller, P. / ...Authors: Wagner, F.F. / Weiwer, M. / Steinbacher, S. / Schomburg, A. / Reinemer, P. / Gale, J.P. / Campbell, A.J. / Fisher, S.L. / Zhao, W.N. / Reis, S.A. / Hennig, K.M. / Thomas, M. / Muller, P. / Jefson, M.R. / Fass, D.M. / Haggarty, S.J. / Zhang, Y.L. / Holson, E.B.
History
DepositionMar 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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: Histone deacetylase 2
B: Histone deacetylase 2
C: Histone deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,27024
Polymers126,6873
Non-polymers2,58321
Water12,556697
1
A: Histone deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1688
Polymers42,2291
Non-polymers9387
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2029
Polymers42,2291
Non-polymers9738
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Histone deacetylase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9017
Polymers42,2291
Non-polymers6726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.297, 98.013, 139.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Histone deacetylase 2 / HD2


Mass: 42229.090 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92769, histone deacetylase

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Non-polymers , 8 types, 718 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-IWX / N-(4-amino-4'-fluoro[1,1'-biphenyl]-3-yl)oxane-4-carboxamide


Mass: 314.354 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H19FN2O2
#5: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 697 / 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: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 400, potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2013 / Details: KB mirror pair
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→80.15 Å / Num. obs: 141832 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 9.42
Reflection shellResolution: 1.66→1.91 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.91 / % possible all: 97.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0135refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→48.35 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.172 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.094 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20778 3303 2.3 %RANDOM
Rwork0.18502 ---
obs0.18556 138529 95.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.947 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2--0.75 Å2-0 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.66→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8866 0 158 697 9721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199273
X-RAY DIFFRACTIONr_bond_other_d0.0030.028606
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.96712493
X-RAY DIFFRACTIONr_angle_other_deg1.196319831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21551105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78623.775453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.779151555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3031551
X-RAY DIFFRACTIONr_chiral_restr0.0820.21268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110501
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022254
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.581.2084417
X-RAY DIFFRACTIONr_mcbond_other0.5791.2074416
X-RAY DIFFRACTIONr_mcangle_it0.9652.0335523
X-RAY DIFFRACTIONr_mcangle_other0.9662.0345524
X-RAY DIFFRACTIONr_scbond_it1.0771.4774856
X-RAY DIFFRACTIONr_scbond_other1.0751.4774856
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6972.3676971
X-RAY DIFFRACTIONr_long_range_B_refined5.7586.37210957
X-RAY DIFFRACTIONr_long_range_B_other5.5395.94410628
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.661→1.704 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 244 -
Rwork0.296 10427 -
obs--97.9 %
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)
10.7375-0.2092-0.32711.20230.12121.3685-0.0262-0.0405-0.0249-0.0431-0.0093-0.01030.03560.04140.03550.061-0.02320.02190.0645-0.00890.064959.03226.302-1.348
21.42980.42-0.03980.8728-0.04341.3107-0.00230.043-0.00510.0067-0.0079-0.0419-0.02290.07240.01030.030.0152-0.00220.01580.00450.044193.12438.545-36.605
31.7431-0.16190.26991.4130.24951.03130.0520.1658-0.0632-0.1959-0.08770.1543-0.0469-0.05120.03570.11080.0271-0.02880.1253-0.03470.131849.48523.393-47.378
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 379
2X-RAY DIFFRACTION2B14 - 379
3X-RAY DIFFRACTION3C14 - 379

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