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- PDB-6tld: Crystal structure of Schistosoma mansoni HDAC8 complexed with a t... -

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Basic information

Entry
Database: PDB / ID: 6tld
TitleCrystal structure of Schistosoma mansoni HDAC8 complexed with a triazole hydroxamate inhibitor 2
ComponentsHistone deacetylase
KeywordsHYDROLASE / Epigenetics / Histone deacetylase / HDAC8 / Selective inhibitor / Pathogen
Function / homology
Function and homology information


histone deacetylase / chromatin organization / 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
DIMETHYLFORMAMIDE / : / Chem-NK5 / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsShaik, T.B. / Romier, C.
Funding support France, 2items
OrganizationGrant numberCountry
European Commission241865 France
European Commission602080 France
CitationJournal: Chemmedchem / Year: 2020
Title: Structure-Based Design, Synthesis, and Biological Evaluation of Triazole-Based smHDAC8 Inhibitors.
Authors: Kalinin, D.V. / Jana, S.K. / Pfafenrot, M. / Chakrabarti, A. / Melesina, J. / Shaik, T.B. / Lancelot, J. / Pierce, R.J. / Sippl, W. / Romier, C. / Jung, M. / Holl, R.
History
DepositionDec 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Histone deacetylase
C: Histone deacetylase
D: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,03050
Polymers202,3324
Non-polymers3,69846
Water17,294960
1
A: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,40711
Polymers50,5831
Non-polymers82410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,53513
Polymers50,5831
Non-polymers95212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,48012
Polymers50,5831
Non-polymers89711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,60814
Polymers50,5831
Non-polymers1,02513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.640, 70.720, 98.050
Angle α, β, γ (deg.)78.080, 75.690, 85.720
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Histone deacetylase /


Mass: 50583.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: HDAC8 / Production host: Escherichia coli (E. coli) / References: UniProt: A5H660

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Non-polymers , 6 types, 1006 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-NK5 / ~{N}-oxidanyl-1-phenyl-1,2,3-triazole-4-carboxamide


Mass: 204.185 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H8N4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-DMF / DIMETHYLFORMAMIDE / Dimethylformamide


Mass: 73.094 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C3H7NO
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 960 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NA,K L-TARTRATE 21% (W/V) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072522 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072522 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 213325 / % possible obs: 92.2 % / Redundancy: 3.6 % / CC1/2: 0.999 / Net I/σ(I): 11.4
Reflection shellResolution: 1.61→1.71 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.04 / Num. unique obs: 32281 / CC1/2: 0.498 / % possible all: 86.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZ5

4bz5


Resolution: 1.61→50 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 21.6
RfactorNum. reflection% reflection
Rfree0.1953 10657 5 %
Rwork0.1659 --
obs0.1674 213108 92.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.63 Å2 / Biso mean: 32.2414 Å2 / Biso min: 14.22 Å2
Refinement stepCycle: final / Resolution: 1.61→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13053 0 228 960 14241
Biso mean--51.78 40.38 -
Num. residues----1633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713749
X-RAY DIFFRACTIONf_angle_d0.85518678
X-RAY DIFFRACTIONf_chiral_restr0.0541989
X-RAY DIFFRACTIONf_plane_restr0.0062448
X-RAY DIFFRACTIONf_dihedral_angle_d13.9248041
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.61-1.6330.35152650.3389504269
1.633-1.65220.31953400.3054644288
1.6522-1.67240.32163370.2918640188
1.6724-1.69350.27323560.2778677992
1.6935-1.71580.28443540.2667671792
1.7158-1.73930.30133520.2627669192
1.7393-1.76420.31093580.28679992
1.7642-1.79050.29253500.2591665792
1.7905-1.81850.27423580.2364679392
1.8185-1.84830.27413540.2286672692
1.8483-1.88020.25093500.2089665892
1.8802-1.91440.23633560.2006675491
1.9144-1.95120.24593440.1929652990
1.9512-1.9910.21683460.1841657890
1.991-2.03430.21723600.1743685193
2.0343-2.08160.19593630.1658689894
2.0816-2.13370.21213570.1681677493
2.1337-2.19140.18333590.1637680993
2.1914-2.25590.18723620.1508689394
2.2559-2.32870.193620.1555686694
2.3287-2.41190.18923620.157687294
2.4119-2.50850.21323540.1614674092
2.5085-2.62260.19793690.1648699896
2.6226-2.76090.19843680.1609700096
2.7609-2.93390.16923720.1522705896
2.9339-3.16040.18633670.1552698696
3.1604-3.47830.18423690.1503701095
3.4783-3.98150.15813670.1392697295
3.9815-5.01550.1473740.1284710097
5.0155-49.82380.19363720.1669705897
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)
10.77550.1927-0.19190.4964-0.29360.62470.0441-0.0834-0.0440.05-0.0603-0.0184-0.02940.0404-00.1823-0.0186-0.01460.22850.00160.182853.227125.191485.612
20.6349-0.1870.10680.3741-0.08980.47830.0026-0.02070.0241-0.0055-0.0155-0.0017-0.0189-0.022800.14350.0068-0.0020.1653-0.00010.173188.42343.361670.2147
30.3898-0.1114-0.08770.75360.04910.4061-0.025-0.0083-0.0004-0.07470.0284-0.0022-0.0159-0.021900.18310.0033-0.010.1470.00260.156444.60692.864540.6465
40.60480.2195-0.19150.6531-0.02280.5333-0.05110.075-0.1093-0.04630.0168-0.04410.00430.0149-00.206-0.00920.0170.1821-0.01460.203165.001436.147125.0336
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 901
2X-RAY DIFFRACTION2chain BB2 - 900
3X-RAY DIFFRACTION3chain CC2 - 901
4X-RAY DIFFRACTION4chain DD2 - 900

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