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- PDB-6ncf: The structure of Stable-5-Lipoxygenase bound to AKBA -

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Basic information

Entry
Database: PDB / ID: 6ncf
TitleThe structure of Stable-5-Lipoxygenase bound to AKBA
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 / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen / Biosynthesis of DPAn-3-derived maresins / arachidonate 12(S)-lipoxygenase activity / negative regulation of sprouting angiogenesis / negative regulation of response to endoplasmic reticulum stress / leukocyte chemotaxis involved in inflammatory response / Biosynthesis of Lipoxins (LX) / 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 / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / arachidonate metabolic process / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / negative regulation of vascular wound healing / lipid oxidation / leukotriene metabolic process / Biosynthesis of maresins / regulation of cellular response to oxidative stress / negative regulation of wound healing / Synthesis of Leukotrienes (LT) and Eoxins (EX) / leukocyte migration involved in inflammatory response / leukotriene biosynthetic process / long-chain fatty acid biosynthetic process / regulation of reactive oxygen species biosynthetic process / regulation of fat cell differentiation / nuclear envelope lumen / regulation of cytokine production involved in inflammatory response / negative regulation of endothelial cell proliferation / humoral immune response / positive regulation of bone mineralization / regulation of insulin secretion / negative regulation of angiogenesis / negative regulation of inflammatory response / nuclear matrix / nuclear envelope / glucose homeostasis / regulation of inflammatory response / Interleukin-4 and Interleukin-13 signaling / secretory granule lumen / nuclear membrane / ficolin-1-rich granule lumen / oxidoreductase activity / 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-AF7 / : / Polyunsaturated fatty acid 5-lipoxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.871 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
DepositionDec 11, 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 1.3Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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
C: Arachidonate 5-lipoxygenase
D: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,4819
Polymers317,7454
Non-polymers7365
Water00
1
A: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4922
Polymers79,4361
Non-polymers561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0053
Polymers79,4361
Non-polymers5692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4922
Polymers79,4361
Non-polymers561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Arachidonate 5-lipoxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4922
Polymers79,4361
Non-polymers561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.870, 203.720, 110.440
Angle α, β, γ (deg.)90.000, 109.710, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -11 or resid 6 through 673))
21(chain B and (resid -11 or resid 6 through 673))
31chain C
41chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid -11 or resid 6 through 673))A0
211(chain B and (resid -11 or resid 6 through 673))B0
311chain CC5 - 673
411chain DD5 - 673

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Components

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


Mass: 79436.242 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AF7 / (3alpha,8alpha,17alpha,18alpha)-3-(acetyloxy)-11-oxours-12-en-23-oic acid


Mass: 512.721 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H48O5
Has protein modificationN
Sequence detailsRESIDUES 41-45 (UNP P09917) 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 8-12% Tacsimate pH 6.0

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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: Jul 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.11
ReflectionResolution: 2.87→103.97 Å / Num. obs: 70741 / % possible obs: 97 % / Redundancy: 3.8 % / CC1/2: 0.982 / Rmerge(I) obs: 0.252 / Rpim(I) all: 0.15 / Rrim(I) all: 0.294 / Net I/σ(I): 5.5 / Num. measured all: 267705 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.87-2.933.21.03537760.650.6621.23379.7
13.76-103.973.60.0446160.9980.0280.05389.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å103.97 Å
Translation3 Å103.97 Å

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
PHASER2.7.16phasing
PHENIX1.12rc2_2821refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.871→50 Å / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 41.17
RfactorNum. reflection% reflection
Rfree0.2972 3609 5.21 %
Rwork0.2747 --
obs0.2776 69332 95.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.36 Å2 / Biso mean: 33.7875 Å2 / Biso min: 6.62 Å2
Refinement stepCycle: final / Resolution: 2.871→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21830 0 88 0 21918
Biso mean--10.94 --
Num. residues----2689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422428
X-RAY DIFFRACTIONf_angle_d0.74930450
X-RAY DIFFRACTIONf_chiral_restr0.0463288
X-RAY DIFFRACTIONf_plane_restr0.0053944
X-RAY DIFFRACTIONf_dihedral_angle_d12.418269
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A13042X-RAY DIFFRACTION12.019TORSIONAL
12B13042X-RAY DIFFRACTION12.019TORSIONAL
13C13042X-RAY DIFFRACTION12.019TORSIONAL
14D13042X-RAY DIFFRACTION12.019TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8752-2.92470.3983950.38711789188449
2.9247-2.97780.36771600.37333304346491
2.9778-3.03510.34871670.32893345351294
3.0351-3.0970.3021870.29723411359893
3.097-3.16420.32481760.29313373354993
3.1642-3.23780.31741690.28193380354994
3.2378-3.31860.30871750.27323386356194
3.3186-3.40820.3211710.27583372354394
3.4082-3.50840.28271850.26553398358393
3.5084-3.62150.28541800.25913366354694
3.6215-3.75070.26262040.2613356356093
3.7507-3.90050.29421600.2553402356294
3.9005-4.07770.31231930.25133366355993
4.0777-4.29210.2421760.24633380355693
4.2921-4.56020.30561940.2593342353692
4.5602-4.91090.29432010.25923301350292
4.9109-5.40260.27371760.26773386356293
5.4026-6.17870.30051720.28483406357893
6.1787-7.7630.27691930.27713390358393
7.763-30.39350.32071750.28143314348990
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.43950.5779-0.31251.77140.39212.1919-0.05040.08750.286-0.37770.05560.7354-0.2994-0.3665-0.02270.4153-0.0589-0.09830.33240.16960.9548-5.8255-7.322431.747
21.72760.0167-0.12490.33440.06160.69260.10950.31560.1988-0.1460.02280.1372-0.11310.0685-0.14320.5947-0.0056-0.02970.28010.02070.37379.256-24.064228.7744
31.4572-0.2201-0.0140.4640.05580.55230.04110.25470.1999-0.12490.07360.0477-0.08350.2116-0.06320.40980.0072-0.03440.1864-0.0180.20434.9434-25.839534.8899
40.5737-0.02080.43022.0606-0.58851.7755-0.0819-0.01870.1319-0.4758-0.0870.4825-0.3362-0.24130.12590.53590.03660.08570.1887-0.03080.7212.6947-7.2955-20.0976
52.0402-0.0796-0.04030.98680.08160.4295-0.02350.11950.0914-0.2547-0.1195-0.3385-0.1276-0.08320.09340.3128-0.00270.00460.28550.04630.32153.5515-25.7835-17.051
63.00740.70191.52751.02-0.34961.82560.10620.5484-0.3524-0.46470.0727-0.17890.25530.3709-0.1290.61310.0071-0.00320.38340.00550.235867.5478-82.794122.7196
70.9485-0.03050.01410.0682-0.06860.1741-0.02580.2913-0.0568-0.0425-0.0360.3028-0.02340.0583-0.00750.1282-0.01550.00820.2967-0.04260.601626.7849-66.375629.9228
80.22780.01020.17430.4067-0.12650.1870.01440.06130.0448-0.2324-0.0229-0.14140.0450.0603-0.00470.36880.02130.04980.3224-0.22231.11286.1463-82.7111-29.2743
90.2050.1387-0.09840.3172-0.11870.34470.00040.0239-0.2109-0.3160.0272-0.31730.0888-0.0288-0.04170.61890.00950.00530.1623-0.01950.62571.0168-66.5537-28.3445
100.12770.0132-0.09390.0796-0.00280.09040.0051-0.1574-0.1018-0.1345-0.0164-0.2630.0631-0.1523-0.00470.59930.018-0.03450.3761-0.0165-0.310445.397-66.3835-22.0426
110.5207-0.3276-0.25090.6322-0.09270.2660.00640.2794-0.1606-0.20490.03980.13260.1663-0.0511-0.00940.2712-0.0162-0.01720.5217-0.05350.118752.344-66.595523.5609
122.2231-0.1873-0.20181.020.01440.34540.05290.45710.0805-0.4013-0.02480.1457-0.15910.04560.02140.44220.0401-0.14550.3631-0.03920.243327.859-24.206-23.1633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -12 through 112 )A-12 - 112
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 187 )A113 - 187
3X-RAY DIFFRACTION3chain 'A' and (resid 188 through 673 )A188 - 673
4X-RAY DIFFRACTION4chain 'B' and (resid -12 through 112 )B-12 - 112
5X-RAY DIFFRACTION5chain 'B' and (resid 188 through 673 )B188 - 673
6X-RAY DIFFRACTION6chain 'C' and (resid 5 through 112 )C5 - 112
7X-RAY DIFFRACTION7chain 'C' and (resid 188 through 673 )C188 - 673
8X-RAY DIFFRACTION8chain 'D' and (resid 5 through 112 )D5 - 112
9X-RAY DIFFRACTION9chain 'D' and (resid 113 through 187 )D113 - 187
10X-RAY DIFFRACTION10chain 'D' and (resid 188 through 673 )D188 - 673
11X-RAY DIFFRACTION11chain 'C' and (resid 113 through 187 )C113 - 187
12X-RAY DIFFRACTION12chain 'B' and (resid 113 through 187 )B113 - 187

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