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- PDB-6gjk: A degradation product of PD 404182 (P2742) bound to Histone Deace... -

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Basic information

Entry
Database: PDB / ID: 6gjk
TitleA degradation product of PD 404182 (P2742) bound to Histone Deacetylase-like Amidohydrolase
ComponentsHistone deacetylase-like amidohydrolase
KeywordsHYDROLASE / HDAH / HDAC / P2742 / PD 404182 / HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE / HISTONE DEACETYLASE / covalent modification
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / epigenetic regulation of gene expression / hydrolase activity / metal ion binding
Similarity search - Function
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
ACETATE ION / 2-(1,4,5,6-tetrahydropyrimidin-2-yl)benzenethiol / : / D-MALATE / DI(HYDROXYETHYL)ETHER / Histone deacetylase-like amidohydrolase
Similarity search - Component
Biological speciesAlcaligenaceae bacterium FB188 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsKraemer, A. / Meyer-Almes, F.J.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2019
Title: Covalent inhibition of histone deacetylase 8 by 3,4-dihydro-2H-pyrimido[1,2-c][1,3]benzothiazin-6-imine.
Authors: Muth, M. / Jansch, N. / Kopranovic, A. / Kramer, A. / Wossner, N. / Jung, M. / Kirschhofer, F. / Meyer-Almes, F.J.
History
DepositionMay 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.3Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone deacetylase-like amidohydrolase
B: Histone deacetylase-like amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,92923
Polymers80,5072
Non-polymers2,42221
Water14,952830
1
A: Histone deacetylase-like amidohydrolase
B: Histone deacetylase-like amidohydrolase
hetero molecules

A: Histone deacetylase-like amidohydrolase
B: Histone deacetylase-like amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,85746
Polymers161,0144
Non-polymers4,84442
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area20120 Å2
ΔGint-187 kcal/mol
Surface area42340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.680, 100.680, 175.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Histone deacetylase-like amidohydrolase / HDAH


Mass: 40253.480 Da / Num. of mol.: 2 / Mutation: H257P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenaceae bacterium FB188 (bacteria)
Gene: hdaH, hdaH1 / Plasmid: pET / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q70I53, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 8 types, 851 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-F0Z / 2-(1,4,5,6-tetrahydropyrimidin-2-yl)benzenethiol


Mass: 192.281 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N2S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 830 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.78 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.25 / Details: 0.1 M Malate-Imidazole buffer pH 5.25, 4 % PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99988 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 1.47→87.77 Å / Num. obs: 152110 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.06 / Net I/σ(I): 10.6
Reflection shellResolution: 1.47→1.5 Å / CC1/2: 0.791 / Rpim(I) all: 0.409

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G1A

5g1a


Resolution: 1.47→87.77 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.388 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.056 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17446 7459 4.9 %RANDOM
Rwork0.14442 ---
obs0.14591 144560 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.193 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å2-0 Å20 Å2
2--0.34 Å20 Å2
3----0.69 Å2
Refinement stepCycle: 1 / Resolution: 1.47→87.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5533 0 144 830 6507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195921
X-RAY DIFFRACTIONr_bond_other_d0.0020.025362
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.968032
X-RAY DIFFRACTIONr_angle_other_deg0.973.00112380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0875758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.49423.216255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.76715842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8251543
X-RAY DIFFRACTIONr_chiral_restr0.0850.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216755
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021224
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_it1.5731.3873007
X-RAY DIFFRACTIONr_mcbond_other1.571.3873005
X-RAY DIFFRACTIONr_mcangle_it2.0082.0893772
X-RAY DIFFRACTIONr_mcangle_other2.0082.093773
X-RAY DIFFRACTIONr_scbond_it2.3051.6512914
X-RAY DIFFRACTIONr_scbond_other2.3051.6512915
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7272.3674261
X-RAY DIFFRACTIONr_long_range_B_refined3.81919.3196900
X-RAY DIFFRACTIONr_long_range_B_other3.58618.8496797
X-RAY DIFFRACTIONr_rigid_bond_restr1.695311280
X-RAY DIFFRACTIONr_sphericity_free28.3625489
X-RAY DIFFRACTIONr_sphericity_bonded10.37511473
LS refinement shellResolution: 1.473→1.511 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 539 -
Rwork0.228 10559 -
obs--99.82 %

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