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- PDB-3jqd: Crystal structure of pteridine reductase 1 (PTR1) from Trypanosom... -

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Basic information

Entry
Database: PDB / ID: 3jqd
TitleCrystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 2-amino-4-oxo-6-phenyl-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile (DX7)
ComponentsPteridine reductase 1
KeywordsOXIDOREDUCTASE / PTERIDINE REDUCTASE / PTR1 / TRYPANOSOMA BRUCEI / SHORT CHAIN DEHYDROGENASE / INHIBITOR
Function / homology
Function and homology information


pteridine reductase / pteridine reductase activity / oxidoreductase activity / nucleotide binding / cytosol
Similarity search - Function
Pteridine reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-DX7 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTulloch, L.B. / Hunter, W.N.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Structure-based design of pteridine reductase inhibitors targeting african sleeping sickness and the leishmaniases.
Authors: Tulloch, L.B. / Martini, V.P. / Iulek, J. / Huggan, J.K. / Lee, J.H. / Gibson, C.L. / Smith, T.K. / Suckling, C.J. / Hunter, W.N.
History
DepositionSep 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
SupersessionJan 19, 2010ID: 3BMJ
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Pteridine reductase 1
B: Pteridine reductase 1
C: Pteridine reductase 1
D: Pteridine reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,78113
Polymers122,7434
Non-polymers4,0389
Water21,5461196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19930 Å2
ΔGint-131.6 kcal/mol
Surface area32120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.641, 90.731, 84.636
Angle α, β, γ (deg.)90.000, 115.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pteridine reductase 1


Mass: 30685.787 Da / Num. of mol.: 4 / Fragment: UNP residues 102-369
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: PTR1, Tb927.8.2210 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q581W1, pteridine reductase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-DX7 / 2-amino-4-oxo-6-phenyl-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile


Mass: 251.243 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H9N5O
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1196 / 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: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 2-3M Sodium acetate, 10-100mM Sodium citrate, pH 4.0-6.0, VAPOR DIFFUSION, temperature 293K
PH range: 4.0-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 20, 2005
Details: Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.6→38.98 Å / Num. obs: 108123 / % possible obs: 81.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.692.90.3322.247843164130.33284.9
1.69-1.7930.2522.945903154990.25284.6
1.79-1.9130.2123.243046144010.21283.6
1.91-2.0730.1882.439422133040.18883
2.07-2.2630.1452.536039120030.14581.7
2.26-2.533.10.0995.233026106970.09980.4
2.53-2.923.20.0718.43015593650.07179.8
2.92-3.583.30.06982557477540.06978.1
3.58-5.063.30.05510.41869457110.05574.7
5.06-38.983.50.0539.31038829760.05371

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.21data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2C7V

2c7v


Resolution: 1.6→38.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.19 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.828 / SU B: 4.284 / SU ML: 0.077 / SU R Cruickshank DPI: 0.115 / SU Rfree: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 5434 5 %RANDOM
Rwork0.179 ---
obs0.181 108063 80.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.28 Å2 / Biso mean: 16.228 Å2 / Biso min: 5.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å2-0.3 Å2
2--1.58 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7404 0 272 1196 8872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227969
X-RAY DIFFRACTIONr_bond_other_d0.0010.025149
X-RAY DIFFRACTIONr_angle_refined_deg1.1542.00810904
X-RAY DIFFRACTIONr_angle_other_deg0.8463.00112646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.26151039
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55224.295305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.036151282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5891549
X-RAY DIFFRACTIONr_chiral_restr0.0570.21291
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028819
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021470
X-RAY DIFFRACTIONr_nbd_refined0.1910.21740
X-RAY DIFFRACTIONr_nbd_other0.1740.25640
X-RAY DIFFRACTIONr_nbtor_refined0.1660.23984
X-RAY DIFFRACTIONr_nbtor_other0.0810.23849
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2862
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1840.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.254
X-RAY DIFFRACTIONr_mcbond_it1.40646538
X-RAY DIFFRACTIONr_mcbond_other0.38342038
X-RAY DIFFRACTIONr_mcangle_it1.69768082
X-RAY DIFFRACTIONr_scbond_it2.54483440
X-RAY DIFFRACTIONr_scangle_it3.357102793
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 420 -
Rwork0.207 7779 -
all-8199 -
obs--84.56 %
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)
10.9106-0.0567-0.09990.4285-0.08160.7380.0093-0.0920.06370.0506-0.0224-0.0627-0.08970.16910.0131-0.0303-0.0271-0.008-0.0330.0039-0.038728.81694.791528.0144
20.69770.0094-0.10940.2833-0.03180.78550.0018-0.1073-0.04530.03790.00070.03550.0184-0.0841-0.0025-0.0248-0.01330.0143-0.02820.0074-0.0457-0.4479-3.359538.5696
30.47150.0953-0.170.3525-0.03550.7916-0.02460.1435-0.0537-0.04930.018-0.02110.03590.00530.0066-0.02620.00540.0135-0.014-0.0123-0.038818.753-5.5379-0.4396
40.53590.01970.02140.54470.23720.5972-0.00220.10960.0243-0.0891-0.04180.0876-0.0634-0.19560.044-0.02550.0255-0.01190.013-0.0079-0.0255-10.44763.7139.1405
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 268
2X-RAY DIFFRACTION2B2 - 268
3X-RAY DIFFRACTION3C2 - 268
4X-RAY DIFFRACTION4D2 - 268

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