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- PDB-4cmc: Crystal structure of pteridine reductase 1 (PTR1) from Trypanosom... -

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Basic information

Entry
Database: PDB / ID: 4cmc
TitleCrystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor and inhibitor
ComponentsPTERIDINE REDUCTASE 1
KeywordsOXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE
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-VS8 / Pteridine reductase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBarrack, K.L. / Hunter, W.N.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Structure-Based Design and Synthesis of Antiparasitic Pyrrolopyrimidines Targeting Pteridine Reductase 1.
Authors: Khalaf, A.I. / Huggan, J.K. / Suckling, C.J. / Gibson, C.L. / Stewart, K. / Giordani, F. / Barrett, M.P. / Wong, P.E. / Barrack, K.L. / Hunter, W.N.
History
DepositionJan 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2Dec 20, 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 1
B: PTERIDINE REDUCTASE 1
C: PTERIDINE REDUCTASE 1
D: PTERIDINE REDUCTASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,18712
Polymers122,6794
Non-polymers4,5088
Water13,763764
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19660 Å2
ΔGint-133.9 kcal/mol
Surface area32600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.192, 89.474, 84.391
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(-0.7854, -0.02659, 0.6184), (-0.03688, -0.9953, -0.08963), (0.6179, -0.09321, 0.7807)3.565, 2.017, -1.116
2given(0.7836, 0.03972, -0.62), (0.03558, -0.9992, -0.01904), (-0.6202, -0.007144, -0.7844)13.69, 0.1388, 39.34
3given(-1, -0.002904, -0.001776), (-0.003065, 0.9951, 0.09909), (0.001479, 0.09909, -0.9951)17.26, -1.865, 38.07

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Components

#1: Protein
PTERIDINE REDUCTASE 1


Mass: 30669.791 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET15B / 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.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-VS8 / N4-cyclohexyl-5,6-diphenyl-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine


Mass: 383.489 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H25N5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 764 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE CONTAINS ADDITIONAL 20 AMINO ACID HISTIDINE TAG AT N-TERMINUS.

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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: 2.06 Å3/Da / Density % sol: 40.29 % / Description: NONE
Crystal growDetails: RESERVOIR CONTAINED 1.7-2.7 M SODIUM ACETATE, 20-50 MM SODIUM CITRATE PH 4.5-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 HG / Detector: CCD / Date: Jul 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→38.57 Å / Num. obs: 83009 / % possible obs: 97.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.4
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.5 / % possible all: 88.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C7V

2c7v


Resolution: 1.85→38.1 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.365 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES WITH INSUFFICIENT ELECTRON DENSITY WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.23007 4177 5 %RANDOM
Rwork0.18353 ---
obs0.1859 78673 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.455 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20.05 Å2
2--2.36 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.85→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7448 0 308 764 8520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197975
X-RAY DIFFRACTIONr_bond_other_d0.0020.027671
X-RAY DIFFRACTIONr_angle_refined_deg1.722.0110882
X-RAY DIFFRACTIONr_angle_other_deg0.8753.00517567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32651006
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1924.342304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.745151250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2951548
X-RAY DIFFRACTIONr_chiral_restr0.0950.21278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219024
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021792
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6211.8564039
X-RAY DIFFRACTIONr_mcbond_other1.6211.8564038
X-RAY DIFFRACTIONr_mcangle_it2.5472.7655040
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9612.1473936
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 260 -
Rwork0.349 4923 -
obs--82.89 %

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