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- PDB-5l8c: Crystal structure of T. brucei PDE-B1 catalytic domain with inhib... -

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Basic information

Entry
Database: PDB / ID: 5l8c
TitleCrystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-039
ComponentsPhosphodiesterase
KeywordsHYDROLASE / parasitic PDE / African Trypanosomiasis / sleeping sickness
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / 3',5'-cyclic-nucleotide phosphodiesterase activity / axoneme / 3',5'-cyclic-AMP phosphodiesterase activity / cell morphogenesis / signal transduction / metal ion binding / cytoplasm
Similarity search - Function
Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / GAF domain ...Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / GAF-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-908 / FORMIC ACID / GUANIDINE / DI(HYDROXYETHYL)ETHER / Phosphodiesterase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.01 Å
AuthorsSingh, A.K. / Anthonyrajah, E.S. / Brown, D.G.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Targeting a Subpocket in Trypanosoma brucei Phosphodiesterase B1 (TbrPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity.
Authors: Blaazer, A.R. / Singh, A.K. / de Heuvel, E. / Edink, E. / Orrling, K.M. / Veerman, J.J.N. / van den Bergh, T. / Jansen, C. / Balasubramaniam, E. / Mooij, W.J. / Custers, H. / Sijm, M. / ...Authors: Blaazer, A.R. / Singh, A.K. / de Heuvel, E. / Edink, E. / Orrling, K.M. / Veerman, J.J.N. / van den Bergh, T. / Jansen, C. / Balasubramaniam, E. / Mooij, W.J. / Custers, H. / Sijm, M. / Tagoe, D.N.A. / Kalejaiye, T.D. / Munday, J.C. / Tenor, H. / Matheeussen, A. / Wijtmans, M. / Siderius, M. / de Graaf, C. / Maes, L. / de Koning, H.P. / Bailey, D.S. / Sterk, G.J. / de Esch, I.J.P. / Brown, D.G. / Leurs, R.
History
DepositionJun 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 23, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3May 8, 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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.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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphodiesterase
B: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,10718
Polymers81,2472
Non-polymers1,86016
Water6,035335
1
A: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4779
Polymers40,6231
Non-polymers8548
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6309
Polymers40,6231
Non-polymers1,0078
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.600, 115.130, 68.630
Angle α, β, γ (deg.)90.00, 108.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1143-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 586 - 916 / Label seq-ID: 28 - 358

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphodiesterase


Mass: 40623.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: residues 565-918 / Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: PDEB1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8WQX9, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

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Non-polymers , 8 types, 351 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5N3
#6: Chemical ChemComp-908 / 4-[5-[(4~{a}~{R},8~{a}~{S})-4-oxidanylidene-3-propan-2-yl-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-yl]-2-methoxy-phenyl]-~{N}-(2-azanyl-2-oxidanylidene-ethyl)benzamide


Mass: 474.552 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H30N4O4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.4 M sodium formate, 0.3 M guanidine, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 8, 2016 / Details: CRL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.01→57.56 Å / Num. obs: 55896 / % possible obs: 99.4 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.6
Reflection shellResolution: 2.01→2.06 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.203 / Mean I/σ(I) obs: 1.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.01→57.06 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 8.835 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.159
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U values refined individually
RfactorNum. reflection% reflectionSelection details
Rfree0.23748 2682 4.8 %RANDOM
Rwork0.19543 ---
obs0.19748 53212 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: mask
Displacement parametersBiso mean: 48.762 Å2
Baniso -1Baniso -2Baniso -3
1-6.71 Å20 Å2-1.1 Å2
2---0.85 Å20 Å2
3----4.24 Å2
Refinement stepCycle: 1 / Resolution: 2.01→57.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5260 0 122 335 5717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195478
X-RAY DIFFRACTIONr_bond_other_d0.0060.025205
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.9547397
X-RAY DIFFRACTIONr_angle_other_deg1.3311947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8475663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52824.163257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81515933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3511535
X-RAY DIFFRACTIONr_chiral_restr0.10.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026363
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021285
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_it3.6924.6162660
X-RAY DIFFRACTIONr_mcbond_other3.6924.6172661
X-RAY DIFFRACTIONr_mcangle_it5.4376.9083319
X-RAY DIFFRACTIONr_mcangle_other5.4366.9113320
X-RAY DIFFRACTIONr_scbond_it4.55.0982818
X-RAY DIFFRACTIONr_scbond_other4.4925.0982818
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6857.4694079
X-RAY DIFFRACTIONr_long_range_B_refined8.69237.4986682
X-RAY DIFFRACTIONr_long_range_B_other8.68937.4976682
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 40948 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 195 -
Rwork0.404 3925 -
obs--99.28 %

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