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

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Basic information

Entry
Database: PDB / ID: 3jqf
TitleCrystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 1,3,5-triazine-2,4,6-triamine (AX2)
Components(Pteridine reductase ...) x 2
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 / nucleoplasm / cytosol / cytoplasm
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 / 1,3,5-triazine-2,4,6-triamine / (4S,5S)-1,2-DITHIANE-4,5-DIOL / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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: 3BMM
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 26, 2012Group: Non-polymer description
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

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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)128,09229
Polymers122,6954
Non-polymers5,39725
Water19,0781059
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23440 Å2
ΔGint-156.1 kcal/mol
Surface area31290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.549, 90.241, 82.407
Angle α, β, γ (deg.)90.000, 115.570, 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

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Pteridine reductase ... , 2 types, 4 molecules ABDC

#1: Protein Pteridine reductase 1


Mass: 30669.791 Da / Num. of mol.: 3 / 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: Protein Pteridine reductase 1


Mass: 30685.787 Da / Num. of mol.: 1 / 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

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Non-polymers , 7 types, 1084 molecules

#3: 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
#4: Chemical
ChemComp-AX2 / 1,3,5-triazine-2,4,6-triamine / Melamine


Mass: 126.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H6N6
#5: Chemical
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Chemical
ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8O2S2
#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1059 / 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: 2.04 Å3/Da / Density % sol: 39.64 %
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: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 17, 2006
Details: Vertically focusing mirror, Rh coated, water cooled
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.6→23.38 Å / Num. obs: 119467 / % possible obs: 92.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.034 / Rsym value: 0.034 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.693.20.3472.153045165410.34788
1.69-1.793.20.2253.250373159280.22589.5
1.79-1.913.10.1365.346964152260.13690.9
1.91-2.0730.0759.743554143550.07592.3
2.07-2.2630.04615.540720134570.04693.4
2.26-2.5330.03420.137031122260.03494.5
2.53-2.922.90.02624.232169109810.02695.4
2.92-3.582.80.0225.52591793680.0296.5
3.58-5.062.60.01828.11927173590.01897.5
5.06-23.382.30.02316.4942840260.02396

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.5data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2C7V

2c7v


Resolution: 1.6→23.38 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.186 / WRfactor Rwork: 0.144 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.884 / SU B: 3.461 / SU ML: 0.06 / SU R Cruickshank DPI: 0.083 / SU Rfree: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.186 5999 5 %RANDOM
Rwork0.145 ---
obs0.147 119437 92.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 97.78 Å2 / Biso mean: 21.438 Å2 / Biso min: 3.39 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å20 Å2-0.76 Å2
2--1.94 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.6→23.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7405 0 336 1059 8800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0228148
X-RAY DIFFRACTIONr_angle_refined_deg1.6012.0111149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73951075
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93924.377313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.237151328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7251550
X-RAY DIFFRACTIONr_chiral_restr0.0990.21337
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025998
X-RAY DIFFRACTIONr_nbd_refined0.2090.24680
X-RAY DIFFRACTIONr_nbtor_refined0.3010.25658
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2983
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.244
X-RAY DIFFRACTIONr_mcbond_it2.04145264
X-RAY DIFFRACTIONr_mcangle_it2.73568231
X-RAY DIFFRACTIONr_scbond_it3.97583247
X-RAY DIFFRACTIONr_scangle_it5.442102871
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1710 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ALOOSE POSITIONAL0.285
BLOOSE POSITIONAL0.315
CLOOSE POSITIONAL0.275
DLOOSE POSITIONAL0.355
ALOOSE THERMAL2.0810
BLOOSE THERMAL2.110
CLOOSE THERMAL2.1210
DLOOSE THERMAL1.9710
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 427 -
Rwork0.293 7909 -
all-8336 -
obs--87.08 %
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)
10.5377-0.02790.07260.37640.06670.5494-0.01890.0696-0.0262-0.02840.0043-0.06290.05520.17990.0145-0.03190.0187-0.0023-0.01630.0019-0.028211.5687-1.73959.3989
20.5638-0.05230.03830.26620.01580.6128-0.00820.0864-0.0046-0.0456-0.01710.02640.003-0.05390.0253-0.0127-0.001-0.0141-0.0495-0.0029-0.0262-17.52776.289-1.3259
30.65070.01840.07970.50680.08830.6747-0.0239-0.15630.03160.10180.0134-0.04370.00240.07450.0105-0.01140.011-0.0176-0.0208-0.0089-0.04631.447.928937.8308
40.5814-0.08180.02610.34520.04180.5002-0.0345-0.103-0.06390.05560.00250.07470.0757-0.15360.032-0.0205-0.01440.0132-0.0139-0.0017-0.0211-27.8174-0.455127.6978
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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