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- PDB-5g5v: Crystal structure of T. brucei PDE-B1 catalytic domain with inhib... -

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Basic information

Entry
Database: PDB / ID: 5g5v
TitleCrystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-038
ComponentsPHOSPHODIESTERASE B1
KeywordsHYDROLASE / PARASITIC PDE / AFRICAN TRYPANOSOMIASIS / SLEEPING SICKNESS
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / axoneme / 3',5'-cyclic-nucleotide phosphodiesterase activity / 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 / GAF-like domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(4AS,8AR)-4-(3-{4-[(3R)-3-HYDROXYPYRROLIDINE-1- / FORMIC ACID / GUANIDINE / Phosphodiesterase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSingh, A.K. / 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 6, 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 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Jan 10, 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 / struct_site
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_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.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: PHOSPHODIESTERASE B1
B: PHOSPHODIESTERASE B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,40032
Polymers81,2472
Non-polymers2,15430
Water8,017445
1
A: PHOSPHODIESTERASE B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,22221
Polymers40,6231
Non-polymers1,59820
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHODIESTERASE B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,17911
Polymers40,6231
Non-polymers55510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.690, 114.781, 64.009
Angle α, β, γ (deg.)90.00, 109.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PHOSPHODIESTERASE B1


Mass: 40623.340 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 565-918
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Variant: LISTER 427 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: Q8WQX9, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

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Non-polymers , 7 types, 475 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-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH5N3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-8Z4 / (4AS,8AR)-4-(3-{4-[(3R)-3-HYDROXYPYRROLIDINE-1-


Mass: 487.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H33N3O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 3.37 Å3/Da / Density % sol: 63.5 % / Description: NONE
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 PH 6.5; VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 4 DEGREES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92819
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Aug 3, 2015 / Details: CRL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.8→88.58 Å / Num. obs: 90889 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4I15

4i15


Resolution: 1.8→88.58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.348 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19872 4449 4.9 %RANDOM
Rwork0.17637 ---
obs0.17748 86430 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 1.8→88.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5280 0 138 445 5863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195502
X-RAY DIFFRACTIONr_bond_other_d0.0020.025281
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9627409
X-RAY DIFFRACTIONr_angle_other_deg0.9972.99112078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.045667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53924.131259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12315942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0811536
X-RAY DIFFRACTIONr_chiral_restr0.0790.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026239
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021364
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_it1.2221.8182668
X-RAY DIFFRACTIONr_mcbond_other1.2221.8192669
X-RAY DIFFRACTIONr_mcangle_it2.0772.7173332
X-RAY DIFFRACTIONr_mcangle_other2.0772.7173333
X-RAY DIFFRACTIONr_scbond_it1.6832.0492834
X-RAY DIFFRACTIONr_scbond_other1.6832.0492835
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7672.9674077
X-RAY DIFFRACTIONr_long_range_B_refined5.45315.2336521
X-RAY DIFFRACTIONr_long_range_B_other5.45315.2366522
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 308 -
Rwork0.28 6340 -
obs--96.78 %

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