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

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Basic information

Entry
Database: PDB / ID: 3jqe
TitleCrystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 2-amino-6-(4-methoxyphenyl)-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile (DX8)
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-DX8 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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: 3BMK
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
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_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_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)126,83713
Polymers122,6794
Non-polymers4,1589
Water14,898827
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19860 Å2
ΔGint-128.8 kcal/mol
Surface area31850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.575, 89.421, 82.372
Angle α, β, γ (deg.)90.000, 115.560, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 268
2116B1 - 268
3116C1 - 268
4116D1 - 268

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Components

#1: Protein
Pteridine reductase 1


Mass: 30669.791 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-DX8 / 2-amino-6-(4-methoxyphenyl)-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile


Mass: 281.269 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H11N5O2
#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.: 827 / 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: 2.02 Å3/Da / Density % sol: 39.1 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→34.32 Å / Num. obs: 62121 / % possible obs: 94.4 % / Redundancy: 5 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 24.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.114.90.2212.44175684400.22188.1
2.11-2.245.10.17734287884160.17793.1
2.24-2.395.10.1413.74097480120.14193.9
2.39-2.585.10.1234.13864975130.12394.6
2.58-2.835.10.114.43583269620.1195.3
2.83-3.165.10.08363255863770.08396.2
3.16-3.6550.06682830456740.06697.1
3.65-4.474.80.05410.32322448270.05497.6
4.47-6.324.70.0549.81769837880.05498.3
6.32-34.324.50.0537.8943221120.05398.1

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Processing

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

2c7v


Resolution: 2→34.32 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.153 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.884 / SU B: 7.037 / SU ML: 0.104 / SU R Cruickshank DPI: 0.188 / SU Rfree: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.213 3179 5.1 %RANDOM
Rwork0.152 ---
obs0.155 62099 94.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 56.22 Å2 / Biso mean: 16.37 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--2.64 Å20 Å2-1.12 Å2
2--3.16 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 2→34.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7413 0 280 827 8520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227969
X-RAY DIFFRACTIONr_angle_refined_deg1.4312.00610901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84151032
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26124.416308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3151274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0141548
X-RAY DIFFRACTIONr_chiral_restr0.0840.21286
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025924
X-RAY DIFFRACTIONr_nbd_refined0.1970.24310
X-RAY DIFFRACTIONr_nbtor_refined0.2980.25506
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2823
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.225
X-RAY DIFFRACTIONr_mcbond_it2.05245182
X-RAY DIFFRACTIONr_mcangle_it2.74168082
X-RAY DIFFRACTIONr_scbond_it4.03383266
X-RAY DIFFRACTIONr_scangle_it5.08102795
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1737 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ALOOSE POSITIONAL0.355
BLOOSE POSITIONAL0.365
CLOOSE POSITIONAL0.35
DLOOSE POSITIONAL0.335
ALOOSE THERMAL2.3410
BLOOSE THERMAL2.3110
CLOOSE THERMAL2.1410
DLOOSE THERMAL2.0410
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 185 -
Rwork0.156 3860 -
all-4045 -
obs--83.45 %
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)
11.6403-0.14470.29920.81410.00791.2471-0.01680.1705-0.0903-0.0244-0.0342-0.05820.10160.23910.051-0.12330.01870.0103-0.0957-0.0139-0.110211.5873-1.68559.573
21.6754-0.17840.11370.3901-0.09951.3555-0.00430.17820.0216-0.0216-0.03090.0546-0.0524-0.06690.0352-0.1173-0.0084-0.0121-0.14390.005-0.1019-17.57086.2217-1.1771
31.86620.17830.22010.55180.19261.4047-0.0502-0.20590.10310.0530.007-0.0233-0.0840.0980.0432-0.10410.0135-0.0138-0.1449-0.0169-0.11051.41447.798238.0435
41.9866-0.05060.2550.602-0.09711.2077-0.0594-0.1294-0.14550.04520.02940.07870.0895-0.20040.03-0.1099-0.01570.0093-0.14140.014-0.0929-27.8828-0.534427.928
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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