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- PDB-2wd8: PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN COMPLEX W... -

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Basic information

Entry
Database: PDB / ID: 2wd8
TitlePTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN COMPLEX WITH NADP AND DDD00071204
ComponentsPTERIDINE REDUCTASE
KeywordsOXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / DRUG DISCOVERY / TRYPANOSOMATIDS / PTERIDINE REDUCTASE / METHOTREXATE RESISTANCE
Function / homology
Function and homology information


pteridine reductase activity / nucleotide binding
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-VGF / Pteridine reductase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRobinson, D.A. / Wyatt, P.G. / Spinks, D. / Brenk, R.
Citation
Journal: J.Med.Chem. / Year: 2009
Title: One Scaffold, Three Binding Modes: Novel and Selective Pteridine Reductase 1 Inhibitors Derived from Fragment Hits Discovered by Virtual Screening.
Authors: Mpamhanga, C.P. / Spinks, D. / Tulloch, L.B. / Shanks, E.J. / Robinson, D.A. / Collie, I.T. / Fairlamb, A.H. / Wyatt, P.G. / Frearson, J.A. / Hunter, W.N. / Gilbert, I.H. / Brenk, R.
#1: Journal: Mol.Microbiol. / Year: 2006
Title: Structure and Reactivity of Trypanosoma Brucei Pteridine Reductase: Inhibition by the Archetypal Antifolate Methotrexate.
Authors: Dawson, A. / Gibellini, F. / Sienkiewicz, N. / Tulloch, L.B. / Fyfe, P.K. / Mcluskey, K. / Fairlamb, A.H. / Hunter, W.N.
History
DepositionMar 20, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 30, 2013Group: Database references / Other
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
B: PTERIDINE REDUCTASE
C: PTERIDINE REDUCTASE
D: PTERIDINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,76813
Polymers113,9944
Non-polymers3,7749
Water13,205733
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18740 Å2
ΔGint-147.22 kcal/mol
Surface area32630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.640, 89.801, 83.061
Angle α, β, γ (deg.)90.00, 115.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.77234, -0.04037, -0.63393), (-0.02861, -0.99475, 0.09821), (-0.63457, 0.09399, 0.76713)-2.46108, 3.76257, -1.03965
2given(0.76711, 0.02815, 0.64089), (0.02648, -0.99957, 0.01221), (0.64096, 0.0076, -0.76753)-13.74795, 5.83686, 37.8665
3given(-0.99997, 0.00633, -0.00349), (0.00666, 0.99466, -0.10302), (0.00282, -0.10304, -0.99467)-16.06685, 1.95278, 37.24812

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Components

#1: Protein
PTERIDINE REDUCTASE


Mass: 28498.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET-TBPTR1H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290, pteridine reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-VGF / 1-(3,4-DICHLOROBENZYL)-7-PHENYL-1H-BENZIMIDAZOL-2-AMINE


Mass: 368.259 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H15Cl2N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 733 / 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: 2.03 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growpH: 4.6 / Details: 1.8M NA ACETATE, 0.1M CITRATE BUFFER PH6.0, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 29, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 48991 / % possible obs: 84.7 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.4 / % possible all: 84.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C7V

2c7v


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.964 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22622 2496 5.1 %RANDOM
Rwork0.15844 ---
obs0.16187 46474 84.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.285 Å2
Baniso -1Baniso -2Baniso -3
1--2.74 Å20 Å2-1.14 Å2
2--3.38 Å20 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7410 0 246 733 8389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227841
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4192.00110701
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79551007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5224.267300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.289151248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3711548
X-RAY DIFFRACTIONr_chiral_restr0.0860.21261
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025826
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.24425
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.25440
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2761
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6151.55137
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0127986
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.68733140
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5414.52703
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.097→2.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 176 -
Rwork0.239 3268 -
obs--80.83 %
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)
11.60660.0881-0.0540.81430.1240.8282-0.03270.1043-0.0691-0.02080.0304-0.17180.0730.18150.0023-0.10870.0138-0.0002-0.1114-0.011-0.087111.6412-1.43579.4804
21.1498-0.0670.2330.78190.11091.4172-0.00830.17980.0569-0.0689-0.01880.0878-0.056-0.09780.027-0.1282-0.0017-0.0028-0.10750.017-0.097-17.46315.9328-1.3349
31.33850.01190.2660.5805-0.21242.1613-0.0182-0.22550.17920.1196-0.0048-0.1145-0.20360.15430.0229-0.1047-0.003-0.0147-0.0496-0.0362-0.07031.25387.821238.0457
41.6426-0.263-0.12030.53950.01461.2284-0.0347-0.1822-0.15450.05490.03090.14660.1108-0.21690.0037-0.1139-0.02590.0007-0.05150.021-0.0852-27.827-0.367828.0032
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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