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- PDB-3bmo: Structure of Pteridine Reductase 1 (PTR1) from Trypanosoma brucei... -

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Basic information

Entry
Database: PDB / ID: 3bmo
TitleStructure of Pteridine Reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor (Compound AX4)
Components(Pteridine reductase) x 2
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 / Chem-AX4 / (4S,5S)-1,2-DITHIANE-4,5-DIOL / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsMartini, V.P. / Iulek, J. / Hunter, W.N. / Tulloch, L.B.
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
DepositionDec 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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)128,53731
Polymers122,6954
Non-polymers5,84127
Water21,8161211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.730, 90.987, 82.818
Angle α, β, γ (deg.)90.00, 115.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACDB

#1: Protein Pteridine reductase


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


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

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Non-polymers , 8 types, 1238 molecules

#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: 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
#6: Chemical
ChemComp-AX4 / 6-[(4-methylphenyl)sulfanyl]pyrimidine-2,4-diamine


Mass: 232.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N4S
#7: Chemical
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2S2
#8: 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
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1211 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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: SYNCHROTRON / Site: SRS / Beamline: PX14.1
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→23.78 Å / Num. obs: 125691 / % possible obs: 96 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.6-1.693.30.32.40.3191.4
1.69-1.793.50.2123.50.212194.2
1.79-1.913.40.1445.20.144194.8
1.91-2.073.40.0888.50.088195.9
2.07-2.263.50.06120.06196.9
2.26-2.533.60.04814.80.048197.9
2.53-2.923.70.03917.30.039198.7
2.92-3.583.60.02919.90.029199.3
3.58-5.063.60.024240.024199.7
5.06-23.783.40.029180.029198.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→22.38 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.261 / SU ML: 0.04 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15029 6280 5 %RANDOM
Rwork0.11836 ---
obs0.11997 119087 95.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.148 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å2-0.36 Å2
2--0.73 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.6→22.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7498 0 367 1211 9076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228523
X-RAY DIFFRACTIONr_bond_other_d0.0010.027929
X-RAY DIFFRACTIONr_angle_refined_deg1.6442.01211696
X-RAY DIFFRACTIONr_angle_other_deg0.8713.00218451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79551163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66924.461334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.262151437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7681554
X-RAY DIFFRACTIONr_chiral_restr0.0940.21380
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029462
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021564
X-RAY DIFFRACTIONr_nbd_refined0.2210.21960
X-RAY DIFFRACTIONr_nbd_other0.1820.28631
X-RAY DIFFRACTIONr_nbtor_refined0.1750.24210
X-RAY DIFFRACTIONr_nbtor_other0.0850.24942
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.21062
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2610.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.246
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2625282
X-RAY DIFFRACTIONr_mcbond_other0.35922140
X-RAY DIFFRACTIONr_mcangle_it2.0938560
X-RAY DIFFRACTIONr_scbond_it2.7454.53321
X-RAY DIFFRACTIONr_scangle_it4.11863050
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 423 -
Rwork0.196 7956 -
obs--89.45 %
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)
10.38510.00450.04580.43910.03990.5026-0.00950.0324-0.0153-0.0120.012-0.06030.02950.1133-0.0025-0.03190.01330.0008-0.0239-0.0013-0.010911.6099-1.4169.3892
20.4313-0.04870.02970.3067-0.01380.4959-0.00280.0542-0.0117-0.0265-0.01320.03130.0015-0.04190.016-0.02220.0025-0.0035-0.0299-0.0029-0.0209-17.2596.5463-1.4455
30.57040.03450.01510.33430.10430.4903-0.0141-0.11690.01860.08210.0118-0.03730.00150.02730.0023-0.01240.005-0.0137-0.0225-0.0051-0.03531.27988.151437.6883
40.3973-0.01830.03050.3690.08480.4833-0.0182-0.0692-0.0420.0387-0.00420.0570.0445-0.12310.0224-0.0319-0.0140.0183-0.0012-0.0005-0.0216-27.7346-0.337127.5912
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 26822 - 288
2X-RAY DIFFRACTION2BB1 - 26821 - 288
3X-RAY DIFFRACTION3CC2 - 26822 - 288
4X-RAY DIFFRACTION4DD2 - 26822 - 288

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