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- PDB-3gn1: Structure of Pteridine Reductase 1 (PTR1) from TRYPANOSOMA BRUCEI... -

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Basic information

Entry
Database: PDB / ID: 3gn1
TitleStructure of Pteridine Reductase 1 (PTR1) from TRYPANOSOMA BRUCEI in ternary complex with cofactor (NADP+) and inhibitor (DDD00067116)
ComponentsPteridine reductase
KeywordsOXIDOREDUCTASE / PTERIDINE REDUCTASE / PTR1 / TRYPANOSOMA BRUCEI / SHORT CHAIN DEHYDROGENASE / INHIBITOR
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
ACETATE ION / 1H-benzimidazol-2-amine / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTulloch, L.B. / Brenk, R. / Hunter, W.N.
CitationJournal: 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.
History
DepositionMar 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 7, 2011Group: Database references
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
B: Pteridine reductase
C: Pteridine reductase
D: Pteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,23413
Polymers122,7434
Non-polymers3,4919
Water16,141896
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20010 Å2
ΔGint-128 kcal/mol
Surface area32510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.641, 90.408, 82.638
Angle α, β, γ (deg.)90.00, 115.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pteridine reductase


Mass: 30685.787 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290
#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-AX7 / 1H-benzimidazol-2-amine


Mass: 133.151 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H7N3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 896 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 39.89 %
Crystal growMethod: vapor diffusion / pH: 4.5
Details: 2-3M SODIUM ACETATE, 10-100MM SODIUM CITRATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→30.66 Å / Num. obs: 63246 / % possible obs: 94.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 9.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 5.1 / Rsym value: 0.136 / % possible all: 89.9

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.66 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.616 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ALL OF THE 17 RELATED STRUCTURES ARE EXPRESSED FROM THE SAME DNA CONSTRUCT, WHICH ENCODES CYS AT POSITIONS 59 AND 168. CRYSTALS HARVESTED WITHIN A COUPLE OF DAYS OF FORMATION CONTAIN CYS AT ...Details: ALL OF THE 17 RELATED STRUCTURES ARE EXPRESSED FROM THE SAME DNA CONSTRUCT, WHICH ENCODES CYS AT POSITIONS 59 AND 168. CRYSTALS HARVESTED WITHIN A COUPLE OF DAYS OF FORMATION CONTAIN CYS AT POSITIONS 59 AND 168. HOWEVER THESE TWO RESIDUES APPEAR QUITE REACTIVE AND OVER TIME BECOME OXIDISED TO CSX, AS DETERMINED BY THE EMERGENCE IN OLDER CRYSTALS OF ELECTRON DENSITY FOR THE OD ATOM. SOMETIMES CYS168 REACTS WITH DTT IN THE CRYSTALLISATION BUFFER, COVALENTLY LINKING THE TWO MOLECULES BY AN S-S BOND.
RfactorNum. reflection% reflection
Rfree0.216 3203 5.1 %
Rwork0.155 --
obs0.158 63194 94.5 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 12.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å2-0.81 Å2
2--1.52 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 2→30.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7417 0 230 896 8543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227882
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.474210766
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04951019
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71524.379306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.362151258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6171548
X-RAY DIFFRACTIONr_chiral_restr0.0910.21281
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025834
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.24247
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.25443
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2884
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.33245156
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.1568043
X-RAY DIFFRACTIONr_scbond_it4.74483088
X-RAY DIFFRACTIONr_scangle_it5.911102706
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å
RfactorNum. reflection% reflection
Rfree0.277 189 -
Rwork0.192 4065 -
obs--86.11 %
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)
10.4099-0.01390.1840.4917-0.07550.5961-0.0110.0873-0.0191-0.0256-0.019-0.0360.05630.1690.03-0.0320.02050.0079-0.0065-0.0032-0.03211.4942-1.64219.4546
20.5207-0.13640.02420.34520.09270.7554-0.02170.0807-0.0174-0.0048-0.02190.0167-0.0177-0.04570.0436-0.02880.0017-0.0091-0.04020.0032-0.0362-17.53196.2459-1.4036
30.83580.03960.07210.4454-0.02540.5028-0.0292-0.11090.05990.01710.0169-0.0096-0.01020.04790.0123-0.01620.0078-0.0142-0.0309-0.0106-0.03891.16787.989237.9548
40.683-0.12520.01070.41640.00210.6643-0.0424-0.035-0.04660.05150.01990.03190.0482-0.13130.0225-0.0286-0.01250.0115-0.0256-0.0048-0.0276-28.064-0.56727.7223
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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