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- PDB-1w0c: Inhibition of Leishmania major pteridine reductase (PTR1) by 2,4,... -

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Basic information

Entry
Database: PDB / ID: 1w0c
TitleInhibition of Leishmania major pteridine reductase (PTR1) by 2,4,6-triaminoquinazoline; structure of the NADP ternary complex.
ComponentsPTERIDINE REDUCTASE
KeywordsOXIDOREDUCTASE / ENZYME INHIBITOR / PTERIN / SHORT-CHAIN REDUCTASE / LEISHMANIA / METHOTREXATE / TRYPANOSOMA / NADP / METHOTREXATE RESISTANCE
Function / homology
Function and homology information


pteridine reductase / 6,7-dihydropteridine reductase activity / pteridine reductase activity / tetrahydrobiopterin biosynthetic process / response to methotrexate / oxidoreductase activity / cytosol
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 / 2,4,6-TRIAMINOQUINAZOLINE / Pteridine reductase 1
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMcluskey, K. / Gibellini, F. / Carvalho, P. / Avery, M. / Hunter, W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Inhibition of Leishmania Major Pteridine Reductase by 2,4,6-Triaminoquinazoline: Structure of the Nadph Ternary Complex
Authors: Mcluskey, K. / Gibellini, F. / Carvalho, P. / Avery, M. / Hunter, W.
History
DepositionJun 2, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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
E: PTERIDINE REDUCTASE
F: PTERIDINE REDUCTASE
G: PTERIDINE REDUCTASE
H: PTERIDINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,70025
Polymers261,1768
Non-polymers7,52417
Water20,1231117
1
A: PTERIDINE REDUCTASE
B: PTERIDINE REDUCTASE
C: PTERIDINE REDUCTASE
D: PTERIDINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,43713
Polymers130,5884
Non-polymers3,8509
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: PTERIDINE REDUCTASE
F: PTERIDINE REDUCTASE
G: PTERIDINE REDUCTASE
H: PTERIDINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,26212
Polymers130,5884
Non-polymers3,6748
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)95.851, 102.945, 146.707
Angle α, β, γ (deg.)90.00, 108.32, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, 0.00046, 0.00029), (0.00046, 1, -0.00287), (-0.00029, -0.00287, -1)
Vector: 1.50039, 0.00254, 1.50101)

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Components

#1: Protein
PTERIDINE REDUCTASE / H REGION METHOTREXATE RESISTANCE PROTEIN


Mass: 32646.971 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: CONTAINS INHIBITOR TAQ / Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Strain: B834 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q01782, pteridine reductase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-TAQ / 2,4,6-TRIAMINOQUINAZOLINE


Mass: 175.191 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C8H9N5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1117 / Source method: isolated from a natural source / Formula: H2O
Compound details5,6,7,8-TETRAHYDROBIOPTERIN + 2NADP+ => BIOPTERIN + 2NADPH.

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 5.4
Details: 11-14% PEG 5000, 100 MM NAAC PH 5.5 AND 40-140 MM CAAC.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2003 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) OR SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 59475 / % possible obs: 91 % / Redundancy: 3.9 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 6.9
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.8 / % possible all: 85.2

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E92

1e92


Resolution: 2.6→30 Å / SU B: 15.271 / SU ML: 0.331 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.3 / ESU R Free: 0.455
Details: THE C-CENTRED ORTHORHOMBIC SPACE GROUP C222 WAS ALSO CONSIDERED BUT THE DATA DID NOT SCALE IN THIS SPACE GROUP.
RfactorNum. reflection% reflectionSelection details
Rfree0.337 4162 5 %RANDOM
Rwork0.267 ---
obs-83228 91 %-
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20.256 Å2
2---0.327 Å20 Å2
3---1.048 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15840 0 501 1117 17458

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