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- PDB-1nas: SEPIAPTERIN REDUCTASE COMPLEXED WITH N-ACETYL SEROTONIN -

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Basic information

Entry
Database: PDB / ID: 1nas
TitleSEPIAPTERIN REDUCTASE COMPLEXED WITH N-ACETYL SEROTONIN
ComponentsSEPIAPTERIN REDUCTASE
KeywordsOXIDOREDUCTASE / SEPIAPTERIN REDUCTASE / SHORT-CHAIN DEHYDROGENASE / SDR FAMILY / N-ACETYL SEROTONIN / TETRAHYDROBIOPTERIN
Function / homology
Function and homology information


pteridine metabolic process / sepiapterin reductase (L-erythro-7,8-dihydrobiopterin-forming) / sepiapterin reductase (NADP+) activity / L-phenylalanine metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / cell morphogenesis involved in neuron differentiation / tetrahydrobiopterin metabolic process / voluntary musculoskeletal movement / tetrahydrobiopterin biosynthetic process ...pteridine metabolic process / sepiapterin reductase (L-erythro-7,8-dihydrobiopterin-forming) / sepiapterin reductase (NADP+) activity / L-phenylalanine metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / cell morphogenesis involved in neuron differentiation / tetrahydrobiopterin metabolic process / voluntary musculoskeletal movement / tetrahydrobiopterin biosynthetic process / norepinephrine metabolic process / serotonin metabolic process / dopamine metabolic process / regulation of multicellular organism growth / protein homodimerization activity / mitochondrion / cytosol
Similarity search - Function
Sepiapterin reductase / : / short chain dehydrogenase / 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
N-ACETYL SEROTONIN / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / OXALOACETATE ION / Sepiapterin reductase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsAuerbach, G. / Herrmann, A. / Bacher, A. / Huber, R.
Citation
Journal: EMBO J. / Year: 1997
Title: The 1.25 A crystal structure of sepiapterin reductase reveals its binding mode to pterins and brain neurotransmitters.
Authors: Auerbach, G. / Herrmann, A. / Gutlich, M. / Fischer, M. / Jacob, U. / Bacher, A. / Huber, R.
#1: Journal: Biol.Chem. / Year: 1997
Title: The Pathway from GTP to Tetrahydrobiopterin: Three-Dimensional Structures of GTP Cyclohydrolase I and 6-Pyruvoyl Tetrahydropterin Synthase
Authors: Auerbach, G. / Nar, H.
History
DepositionMar 26, 1998Processing site: BNL
Revision 1.0Mar 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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.process_site / _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: SEPIAPTERIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7414
Polymers27,6491
Non-polymers1,0933
Water7,422412
1
A: SEPIAPTERIN REDUCTASE
hetero molecules

A: SEPIAPTERIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4838
Polymers55,2972
Non-polymers2,1856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area8270 Å2
ΔGint-50 kcal/mol
Surface area19240 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.960, 116.960, 105.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein SEPIAPTERIN REDUCTASE


Mass: 27648.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: BRAIN / Production host: Escherichia coli (E. coli)
References: UniProt: Q64105, sepiapterin reductase (L-erythro-7,8-dihydrobiopterin-forming)
#2: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3O5
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-ASE / N-ACETYL SEROTONIN


Mass: 218.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O

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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: 3.66 Å3/Da / Density % sol: 66 %
Crystal growpH: 4.7 / Details: pH 4.7
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.5 mg/mlprotein1drop
220 mMMES1drop
31 mMdithiothreitol1drop
410 mMNADP1drop
51.5 Mammonium sulfate1reservoir
60.1 Mcitrate1reservoir

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorDate: Oct 23, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 23193 / % possible obs: 93.2 % / Observed criterion σ(I): 0
Reflection
*PLUS
Num. measured all: 167681 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 88.4 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementResolution: 2.1→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.202 -5 %RANDOM
Rwork0.166 ---
obs0.166 22742 --
Displacement parametersBiso mean: 20.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1935 0 73 412 2420
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.738
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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