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- PDB-3qj5: S-nitrosoglutathione reductase (GSNOR) in complex with N6022 -

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Basic information

Entry
Database: PDB / ID: 3qj5
TitleS-nitrosoglutathione reductase (GSNOR) in complex with N6022
ComponentsAlcohol dehydrogenase class-3
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / S-NITROSOGLUTATHIONE REDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


formaldehyde dehydrogenase activity / S-(hydroxymethyl)glutathione dehydrogenase / S-(hydroxymethyl)glutathione dehydrogenase NADP activity / S-(hydroxymethyl)glutathione dehydrogenase NAD activity / S-(hydroxymethyl)glutathione dehydrogenase activity / fatty acid omega-oxidation / formaldehyde catabolic process / response to nitrosative stress / Ethanol oxidation / respiratory system process ...formaldehyde dehydrogenase activity / S-(hydroxymethyl)glutathione dehydrogenase / S-(hydroxymethyl)glutathione dehydrogenase NADP activity / S-(hydroxymethyl)glutathione dehydrogenase NAD activity / S-(hydroxymethyl)glutathione dehydrogenase activity / fatty acid omega-oxidation / formaldehyde catabolic process / response to nitrosative stress / Ethanol oxidation / respiratory system process / alcohol dehydrogenase activity, zinc-dependent / ethanol oxidation / alcohol dehydrogenase / positive regulation of blood pressure / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / response to redox state / retinoid metabolic process / peptidyl-cysteine S-nitrosylation / fatty acid binding / response to lipopolysaccharide / electron transfer activity / mitochondrion / extracellular exosome / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Alcohol dehydrogenase class III / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Zinc-binding dehydrogenase / Alcohol dehydrogenase-like, C-terminal / Alcohol dehydrogenase GroES-like domain / Alcohol dehydrogenase, N-terminal / GroES-like superfamily ...Alcohol dehydrogenase class III / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Zinc-binding dehydrogenase / Alcohol dehydrogenase-like, C-terminal / Alcohol dehydrogenase GroES-like domain / Alcohol dehydrogenase, N-terminal / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-022 / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PENTANE-1,5-DIAMINE / Alcohol dehydrogenase class-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.9 Å
AuthorsChun, L. / Kim, H. / Sun, X.
CitationJournal: ACS Med Chem Lett / Year: 2011
Title: Discovery of s-nitrosoglutathione reductase inhibitors: potential agents for the treatment of asthma and other inflammatory diseases.
Authors: Sun, X. / Wasley, J.W. / Qiu, J. / Blonder, J.P. / Stout, A.M. / Green, L.S. / Strong, S.A. / Colagiovanni, D.B. / Richards, J.P. / Mutka, S.C. / Chun, L. / Rosenthal, G.J.
History
DepositionJan 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alcohol dehydrogenase class-3
B: Alcohol dehydrogenase class-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,09519
Polymers79,4562
Non-polymers3,63917
Water13,331740
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-32 kcal/mol
Surface area27800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.858, 78.858, 310.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alcohol dehydrogenase class-3 / Alcohol dehydrogenase 5 / Alcohol dehydrogenase class chi chain / Alcohol dehydrogenase class-III / ...Alcohol dehydrogenase 5 / Alcohol dehydrogenase class chi chain / Alcohol dehydrogenase class-III / Glutathione-dependent formaldehyde dehydrogenase / FALDH / FDH / GSH-FDH / S-(hydroxymethyl)glutathione dehydrogenase


Mass: 39728.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADH5, ADHX, FDH / Plasmid: VCID 1792 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P11766, alcohol dehydrogenase, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, S-(hydroxymethyl)glutathione dehydrogenase

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Non-polymers , 8 types, 757 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical ChemComp-022 / 3-{1-(4-carbamoyl-2-methylphenyl)-5-[4-(1H-imidazol-1-yl)phenyl]-1H-pyrrol-2-yl}propanoic acid / N6022


Mass: 414.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H22N4O3
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-N2P / PENTANE-1,5-DIAMINE / Cadaverine


Mass: 102.178 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H14N2
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 740 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details1PE IS THE ORDERED PART OF PEG 8000

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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: 3.03 Å3/Da / Density % sol: 59.45 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 19% PEG 8000, 100MM K-PHOSPHATE PH 7.0, 100MM ZNSO4, 1MM DTT, 3% (W/V) BUTANEDIOL, TEMPERATURE 290K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 78296 / Num. obs: 78296 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.95 Å / % possible all: 94.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacement
Starting model: native GSNOR structure

Resolution: 1.9→49.09 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.765 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 3927 5 %RANDOM
Rwork0.184 ---
all0.185 78296 --
obs0.185 77982 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5539 0 233 740 6512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225904
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2592.0097985
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6175753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85724.819193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99315997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2591518
X-RAY DIFFRACTIONr_chiral_restr0.0740.2911
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024254
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1860.22949
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.24029
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2671
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0280.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3991.53696
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.77725963
X-RAY DIFFRACTIONr_scbond_it1.2932226
X-RAY DIFFRACTIONr_scangle_it2.2634.52017
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 272 -
Rwork0.248 5159 -
obs--95.06 %

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