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- PDB-6n2w: The structure of Stable-5-Lipoxygenase bound to NDGA -

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Basic information

Entry
Database: PDB / ID: 6n2w
TitleThe structure of Stable-5-Lipoxygenase bound to NDGA
ComponentsArachidonate 5-lipoxygenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Lipoxygenase / inhibitor / allostery / complex / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


arachidonate 5-lipoxygenase / regulation of inflammatory response to wounding / leukotriene A4 biosynthetic process / lipoxin biosynthetic process / Biosynthesis of DPAn-3-derived protectins and resolvins / Biosynthesis of DPAn-3-derived 13-series resolvins / arachidonate 8(S)-lipoxygenase activity / leukotriene production involved in inflammatory response / arachidonate 5-lipoxygenase activity / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives ...arachidonate 5-lipoxygenase / regulation of inflammatory response to wounding / leukotriene A4 biosynthetic process / lipoxin biosynthetic process / Biosynthesis of DPAn-3-derived protectins and resolvins / Biosynthesis of DPAn-3-derived 13-series resolvins / arachidonate 8(S)-lipoxygenase activity / leukotriene production involved in inflammatory response / arachidonate 5-lipoxygenase activity / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Biosynthesis of DPAn-3-derived maresins / arachidonate 12(S)-lipoxygenase activity / leukocyte chemotaxis involved in inflammatory response / Synthesis of Lipoxins (LX) / negative regulation of response to endoplasmic reticulum stress / negative regulation of sprouting angiogenesis / Synthesis of 5-eicosatetraenoic acids / positive regulation of leukocyte adhesion to arterial endothelial cell / lipoxygenase pathway / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / Interleukin-18 signaling / dendritic cell migration / arachidonic acid metabolic process / negative regulation of vascular wound healing / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / lipid oxidation / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Biosynthesis of maresins / regulation of cellular response to oxidative stress / leukotriene metabolic process / negative regulation of wound healing / hepoxilin biosynthetic process / leukocyte migration involved in inflammatory response / Synthesis of Leukotrienes (LT) and Eoxins (EX) / linoleic acid metabolic process / leukotriene biosynthetic process / regulation of reactive oxygen species biosynthetic process / long-chain fatty acid biosynthetic process / regulation of fat cell differentiation / nuclear envelope lumen / negative regulation of endothelial cell proliferation / regulation of cytokine production involved in inflammatory response / regulation of insulin secretion / humoral immune response / positive regulation of bone mineralization / negative regulation of angiogenesis / negative regulation of inflammatory response / nuclear matrix / glucose homeostasis / nuclear envelope / regulation of inflammatory response / Interleukin-4 and Interleukin-13 signaling / nuclear membrane / secretory granule lumen / ficolin-1-rich granule lumen / hydrolase activity / iron ion binding / Neutrophil degranulation / perinuclear region of cytoplasm / extracellular space / extracellular region / nucleoplasm / cytosol
Similarity search - Function
Lipoxygenase, vertebrates, PLAT domain / Lipoxygenase, mammalian / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase ...Lipoxygenase, vertebrates, PLAT domain / Lipoxygenase, mammalian / Lipoxygenase, conserved site / Lipoxygenases iron-binding region signature 2. / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile.
Similarity search - Domain/homology
Chem-30Z / : / Polyunsaturated fatty acid 5-lipoxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsNewcomer, M.E. / Gilbert, N.C. / Neau, D.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL107887 United States
American Heart Association16GRNT31000010 United States
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Structural and mechanistic insights into 5-lipoxygenase inhibition by natural products.
Authors: Gilbert, N.C. / Gerstmeier, J. / Schexnaydre, E.E. / Borner, F. / Garscha, U. / Neau, D.B. / Werz, O. / Newcomer, M.E.
History
DepositionNov 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arachidonate 5-lipoxygenase
B: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,2875
Polymers158,8722
Non-polymers4143
Water3,081171
1
A: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4922
Polymers79,4361
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7943
Polymers79,4361
Non-polymers3582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.152, 204.358, 76.712
Angle α, β, γ (deg.)90.000, 99.906, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Arachidonate 5-lipoxygenase / / 5-lipoxygenase


Mass: 79436.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALOX5, LOG5 / Production host: Escherichia coli (E. coli) / References: UniProt: P09917, arachidonate 5-lipoxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-30Z / 4-[(2R,3S)-3-[(3,4-DIHYDROXYPHENYL)METHYL]-2-METHYLBUTYL]BENZENE-1,2-DIOL


Mass: 302.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsRESIDUES 41-45 WERE DELETED AND REPLACED WITH GS

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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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 8-10% Tacsimate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.709→102.18 Å / Num. obs: 148992 / % possible obs: 98.24 % / Redundancy: 3.7 % / Biso Wilson estimate: 51.61 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.2695 / Rpim(I) all: 0.1597 / Net I/σ(I): 6.78
Reflection shellResolution: 2.713→2.809 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.454 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 12579 / CC1/2: 0.325 / Rpim(I) all: 0.877 / % possible all: 89.09

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3o8y monomer

3o8y


Resolution: 2.71→75.57 Å / SU ML: 0.5073 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.119
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2626 3853 5.12 %
Rwork0.2129 71400 -
obs0.2155 75253 95.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.54 Å2
Refinement stepCycle: LAST / Resolution: 2.71→75.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9844 0 24 171 10039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006710121
X-RAY DIFFRACTIONf_angle_d0.824713743
X-RAY DIFFRACTIONf_chiral_restr0.14441493
X-RAY DIFFRACTIONf_plane_restr0.00461772
X-RAY DIFFRACTIONf_dihedral_angle_d14.51073741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.740.3229650.28741314X-RAY DIFFRACTION49.04
2.74-2.780.35041370.32132584X-RAY DIFFRACTION96.8
2.78-2.810.33491400.33762599X-RAY DIFFRACTION97.68
2.81-2.850.35781360.34742612X-RAY DIFFRACTION97.17
2.85-2.890.38271340.34822534X-RAY DIFFRACTION97.87
2.89-2.940.41411420.34172608X-RAY DIFFRACTION97.73
2.94-2.980.38511440.34022622X-RAY DIFFRACTION97.5
2.98-3.030.36321400.34472620X-RAY DIFFRACTION97.98
3.03-3.080.3561400.31562563X-RAY DIFFRACTION97.76
3.08-3.140.39651420.30162592X-RAY DIFFRACTION97.71
3.14-3.20.33391390.27542684X-RAY DIFFRACTION98.16
3.2-3.260.31350.26082525X-RAY DIFFRACTION98.48
3.26-3.330.28751460.25652673X-RAY DIFFRACTION98.57
3.34-3.410.30131410.2312593X-RAY DIFFRACTION98.7
3.41-3.50.2731420.22472627X-RAY DIFFRACTION98.72
3.5-3.590.28621390.21312608X-RAY DIFFRACTION98.96
3.59-3.70.28941400.2012659X-RAY DIFFRACTION98.59
3.7-3.820.26951400.19072570X-RAY DIFFRACTION98.62
3.82-3.950.24621450.18842625X-RAY DIFFRACTION98.4
3.95-4.110.20731370.16842602X-RAY DIFFRACTION98.42
4.11-4.30.25211450.17192611X-RAY DIFFRACTION98.43
4.3-4.530.23321380.16092582X-RAY DIFFRACTION97
4.53-4.810.2111450.15462612X-RAY DIFFRACTION96.84
4.81-5.180.17431380.15752543X-RAY DIFFRACTION96.86
5.18-5.70.2831400.17622562X-RAY DIFFRACTION97.4
5.7-6.530.19731410.17742622X-RAY DIFFRACTION98.08
6.53-8.220.20171420.18042586X-RAY DIFFRACTION97.22
8.22-75.570.19771400.16932468X-RAY DIFFRACTION93.21

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