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- PDB-5fue: Crystal structure of Schistosoma mansoni HDAC8 complexed with 3- ... -

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Basic information

Entry
Database: PDB / ID: 5fue
TitleCrystal structure of Schistosoma mansoni HDAC8 complexed with 3- benzamido-benzohydroxamate
ComponentsHISTONE DEACETYLASE 8
KeywordsHYDROLASE / PLATYHELMINTHS / INHIBITION / HISTONE / DEACETYLATION
Function / homology
Function and homology information


histone deacetylase / histone deacetylase activity / heterochromatin formation / metal ion binding / nucleus
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 / : / 3-(benzoylamino)-N-oxobenzamide / histone deacetylase
Similarity search - Component
Biological speciesSCHISTOSOMA MANSONI (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.199 Å
AuthorsMarek, M. / Romier, C.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Structure-Based Design and Synthesis of Novel Inhibitors Targeting Hdac8 from Schistosoma Mansoni for the Treatment of Schistosomiasis.
Authors: Heimburg, T. / Chakrabarti, A. / Lancelot, J. / Marek, M. / Melesina, J. / Hauser, A.T. / Shaik, T.B. / Duclaud, S. / Robaa, D. / Erdmann, F. / Schmidt, M. / Romier, C. / Pierce, R.J. / Jung, M. / Sippl, W.
History
DepositionJan 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Apr 6, 2016Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISTONE DEACETYLASE 8
B: HISTONE DEACETYLASE 8
C: HISTONE DEACETYLASE 8
D: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,56534
Polymers201,7804
Non-polymers2,78630
Water9,296516
1
A: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0277
Polymers50,4451
Non-polymers5826
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0818
Polymers50,4451
Non-polymers6367
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,26510
Polymers50,4451
Non-polymers8209
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: HISTONE DEACETYLASE 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1929
Polymers50,4451
Non-polymers7478
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.955, 70.669, 98.656
Angle α, β, γ (deg.)77.99, 75.41, 85.40
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 8


Mass: 50444.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHISTOSOMA MANSONI (invertebrata) / Plasmid: PNEA-TH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5H660

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Non-polymers , 6 types, 546 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-UV4 / 3-(benzoylamino)-N-oxobenzamide


Mass: 254.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H10N2O3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H7NO
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.32 Å3/Da / Density % sol: 47.02 % / Description: NONE
Crystal growDetails: 0.2 M NA,K L-TARTRATE 21% (W/V) PEG3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.07812
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 88530 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 23.93 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.88
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.75 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.199→42.145 Å / SU ML: 0.2 / σ(F): 2.02 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1957 4524 5.1 %
Rwork0.1476 --
obs0.1501 88494 95.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.37 Å2
Refinement stepCycle: LAST / Resolution: 2.199→42.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12946 0 167 516 13629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713504
X-RAY DIFFRACTIONf_angle_d0.9818348
X-RAY DIFFRACTIONf_dihedral_angle_d13.6894825
X-RAY DIFFRACTIONf_chiral_restr0.0391961
X-RAY DIFFRACTIONf_plane_restr0.0052345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1992-2.22410.19551670.14952485X-RAY DIFFRACTION85
2.2241-2.25030.25381560.15192760X-RAY DIFFRACTION95
2.2503-2.27780.19831430.14672772X-RAY DIFFRACTION94
2.2778-2.30660.24591360.14752758X-RAY DIFFRACTION95
2.3066-2.33690.21211340.14472794X-RAY DIFFRACTION95
2.3369-2.36890.24221520.14612794X-RAY DIFFRACTION94
2.3689-2.40280.21711520.13972772X-RAY DIFFRACTION96
2.4028-2.43860.20541420.13972750X-RAY DIFFRACTION95
2.4386-2.47670.21791700.14832791X-RAY DIFFRACTION96
2.4767-2.51730.21181420.15642773X-RAY DIFFRACTION95
2.5173-2.56070.21981560.1572729X-RAY DIFFRACTION95
2.5607-2.60730.22481660.15192836X-RAY DIFFRACTION96
2.6073-2.65740.23371390.15172796X-RAY DIFFRACTION96
2.6574-2.71170.21851620.14862773X-RAY DIFFRACTION96
2.7117-2.77060.21061580.1462769X-RAY DIFFRACTION96
2.7706-2.83510.21561460.15042861X-RAY DIFFRACTION96
2.8351-2.9060.21451550.14692788X-RAY DIFFRACTION97
2.906-2.98450.22911430.15472806X-RAY DIFFRACTION97
2.9845-3.07230.20611320.15342865X-RAY DIFFRACTION97
3.0723-3.17140.20021490.15912821X-RAY DIFFRACTION98
3.1714-3.28470.1971530.15762839X-RAY DIFFRACTION97
3.2847-3.41620.20141260.15622869X-RAY DIFFRACTION97
3.4162-3.57160.1961800.15042836X-RAY DIFFRACTION98
3.5716-3.75980.18631610.15242834X-RAY DIFFRACTION98
3.7598-3.99520.17121470.13282846X-RAY DIFFRACTION98
3.9952-4.30340.16761410.13232852X-RAY DIFFRACTION98
4.3034-4.73590.1561410.12632881X-RAY DIFFRACTION98
4.7359-5.420.17641490.13972860X-RAY DIFFRACTION98
5.42-6.82390.17741740.16732831X-RAY DIFFRACTION98
6.8239-42.15270.16891520.1552829X-RAY DIFFRACTION97
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)
10.73830.0487-0.13520.3966-0.18780.5404-0.0156-0.084-0.03290.0118-0.0147-0.03270.01060.014-00.0937-0.0062-0.01110.13370.0050.104953.792225.356786.0988
20.703-0.25010.02180.3065-0.0090.4070.0142-0.02550.0243-0.0298-0.0249-0.0197-0.0153-0.007900.04-0.0025-0.00520.0703-0.00310.069388.945643.319670.3147
30.2937-0.0915-0.07850.8520.10860.4029-0.0293-0.0249-0.0311-0.09940.01350.0235-0.0247-0.02750.00010.10530.0022-0.00770.06920.00250.077544.49142.210641.0466
40.45150.1472-0.2790.75640.05530.6266-0.03870.0319-0.0627-0.07190.0115-0.0425-0.00340.0067-0.00010.1074-0.01180.01390.0734-0.00830.082965.05435.681725.3057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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