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- PDB-2q7r: Crystal structure of human FLAP with an iodinated analog of MK-591 -

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Basic information

Entry
Database: PDB / ID: 2q7r
TitleCrystal structure of human FLAP with an iodinated analog of MK-591
ComponentsArachidonate 5-lipoxygenase-activating protein
KeywordsMEMBRANE PROTEIN / LIPID TRANSPORT / FLAP / MAPEG
Function / homology
Function and homology information


leukotriene production involved in inflammatory response / arachidonate 5-lipoxygenase activity / leukotriene-C4 synthase activity / Synthesis of Lipoxins (LX) / Synthesis of 5-eicosatetraenoic acids / lipoxygenase pathway / Synthesis of Leukotrienes (LT) and Eoxins (EX) / positive regulation of acute inflammatory response / leukotriene biosynthetic process / glutathione peroxidase activity ...leukotriene production involved in inflammatory response / arachidonate 5-lipoxygenase activity / leukotriene-C4 synthase activity / Synthesis of Lipoxins (LX) / Synthesis of 5-eicosatetraenoic acids / lipoxygenase pathway / Synthesis of Leukotrienes (LT) and Eoxins (EX) / positive regulation of acute inflammatory response / leukotriene biosynthetic process / glutathione peroxidase activity / arachidonic acid binding / protein homotrimerization / glutathione transferase activity / enzyme activator activity / cellular response to calcium ion / nuclear envelope / nuclear membrane / protein-containing complex binding / endoplasmic reticulum membrane / enzyme binding / endoplasmic reticulum / membrane / identical protein binding
Similarity search - Function
5-lipoxygenase-activating protein / FLAP/GST2/LTC4S, conserved site / FLAP/GST2/LTC4S family signature. / Membrane associated eicosanoid/glutathione metabolism-like domain / Membrane-associated, eicosanoid/glutathione metabolism (MAPEG) protein / Membrane associated eicosanoid/glutathione metabolism-like domain superfamily / MAPEG family / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-3CS / Arachidonate 5-lipoxygenase-activating protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4 Å
AuthorsFerguson, A.D.
CitationJournal: Science / Year: 2007
Title: Crystal structure of inhibitor-bound human 5-lipoxygenase-activating protein.
Authors: Ferguson, A.D. / McKeever, B.M. / Xu, S. / Wisniewski, D. / Miller, D.K. / Yamin, T.T. / Spencer, R.H. / Chu, L. / Ujjainwalla, F. / Cunningham, B.R. / Evans, J.F. / Becker, J.W.
History
DepositionJun 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arachidonate 5-lipoxygenase-activating protein
B: Arachidonate 5-lipoxygenase-activating protein
C: Arachidonate 5-lipoxygenase-activating protein
D: Arachidonate 5-lipoxygenase-activating protein
E: Arachidonate 5-lipoxygenase-activating protein
F: Arachidonate 5-lipoxygenase-activating protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,64712
Polymers109,5166
Non-polymers4,1326
Water0
1
A: Arachidonate 5-lipoxygenase-activating protein
B: Arachidonate 5-lipoxygenase-activating protein
C: Arachidonate 5-lipoxygenase-activating protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8246
Polymers54,7583
Non-polymers2,0663
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
MethodPISA
2
D: Arachidonate 5-lipoxygenase-activating protein
E: Arachidonate 5-lipoxygenase-activating protein
F: Arachidonate 5-lipoxygenase-activating protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8246
Polymers54,7583
Non-polymers2,0663
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.660, 180.660, 139.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsThe biological unit is a trimer

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Components

#1: Protein
Arachidonate 5-lipoxygenase-activating protein / FLAP / MK-886-binding protein


Mass: 18252.596 Da / Num. of mol.: 6 / Mutation: K148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALOX5AP, FLAP / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20292
#2: Chemical
ChemComp-3CS / 3-[3-(3,3-DIMETHYLBUTANOYL)-1-(4-IODOBENZYL)-5-(QUINOLIN-2-YLMETHOXY)-1H-INDOL-2-YL]-2,2-DIMETHYLPROPANOIC ACID


Mass: 688.594 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C36H37IN2O4

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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: 5.21 Å3/Da / Density % sol: 76.41 %
Crystal growTemperature: 298 K / pH: 5.6
Details: 10% PEG 4000, 0.32 LiCl2, 1 mM TCEP, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9797
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 4→45 Å / Num. obs: 20007 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 15.5 % / Biso Wilson estimate: 98.721 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 20.6
Reflection shellResolution: 4→4.24 Å / Redundancy: 15.5 % / Mean I/σ(I) obs: 3.29 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER-TNT1.9.3refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2811 1011 5.09 %RANDOM
Rwork0.2675 ---
obs0.2682 19874 99.54 %-
all-20007 --
Displacement parametersBiso mean: 120.76 Å2
Baniso -1Baniso -2Baniso -3
1--3.39650978 Å20 Å20 Å2
2---3.39650978 Å20 Å2
3---6.79301956 Å2
Refinement stepCycle: LAST / Resolution: 4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6996 0 258 0 7254
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00674602
X-RAY DIFFRACTIONt_angle_deg0.72101342
X-RAY DIFFRACTIONt_dihedral_angle_d29.64713020
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0052162
X-RAY DIFFRACTIONt_gen_planes0.0110925
X-RAY DIFFRACTIONt_it3.463746020
X-RAY DIFFRACTIONt_nbd0.0555895
LS refinement shellResolution: 4→4.24 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.316 143 4.56 %
Rwork0.3105 2993 -
all0.3108 3136 -
obs--99.54 %

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