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

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Basic information

Entry
Database: PDB / ID: 4cmk
TitleCrystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor and inhibitor
ComponentsPTERIDINE REDUCTASE 1
KeywordsOXIDOREDUCTASE / PTR1 / 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
ACETATE ION / Chem-FQW / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2 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 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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)127,03313
Polymers122,6794
Non-polymers4,3549
Water10,251569
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23370 Å2
ΔGint-159.7 kcal/mol
Surface area31430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.541, 90.275, 82.329
Angle α, β, γ (deg.)90.00, 115.54, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.7785, -0.02868, -0.627), (-0.03772, -0.995, 0.09236), (-0.6265, 0.09555, 0.7735)-2.598, 3.964, -1.121
2given(0.773, 0.01927, 0.6341), (0.01857, -0.9998, 0.007754), (0.6341, 0.005782, -0.7732)-13.62, 5.938, 37.88
3given(-0.9999, 0.01241, -0.00251), (0.0126, 0.995, -0.09884), (0.001271, -0.09887, -0.9951)-16.11, 1.978, 37.21

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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) / 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-FQW / 2-amino-5-phenethyl-6-phenyl-3H-pyrrolo[2,3-d]pyrimidin-4(7H)-one


Mass: 330.383 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H18N4O
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 2.04 Å3/Da / Density % sol: 39.63 % / 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: Dec 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→45.14 Å / Num. obs: 66280 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2→45.14 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.858 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23316 3385 5.1 %RANDOM
Rwork0.1731 ---
obs0.17614 62873 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.081 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20 Å2-0.46 Å2
2--2.63 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7467 0 296 569 8332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0197898
X-RAY DIFFRACTIONr_bond_other_d0.0020.027596
X-RAY DIFFRACTIONr_angle_refined_deg1.9192.00810762
X-RAY DIFFRACTIONr_angle_other_deg0.871317379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5015990
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94224.342304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.538151245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8261548
X-RAY DIFFRACTIONr_chiral_restr0.0980.21262
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021778
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_it1.6031.7583997
X-RAY DIFFRACTIONr_mcbond_other1.6031.7583995
X-RAY DIFFRACTIONr_mcangle_it2.5362.6164974
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8952.0193901
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: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 254 -
Rwork0.276 4632 -
obs--99.23 %

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