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- PDB-7av2: LTA4 hydrolase in complex with fragment1 -

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Basic information

Entry
Database: PDB / ID: 7av2
TitleLTA4 hydrolase in complex with fragment1
ComponentsLeukotriene A-4 hydrolase
KeywordsHYDROLASE / Inhibitor / complex
Function / homology
Function and homology information


leukotriene-A4 hydrolase / tripeptide aminopeptidase / tripeptide aminopeptidase activity / leukotriene-A4 hydrolase activity / Biosynthesis of protectins / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Synthesis of Leukotrienes (LT) and Eoxins (EX) ...leukotriene-A4 hydrolase / tripeptide aminopeptidase / tripeptide aminopeptidase activity / leukotriene-A4 hydrolase activity / Biosynthesis of protectins / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / Synthesis of Leukotrienes (LT) and Eoxins (EX) / protein metabolic process / epoxide hydrolase activity / leukotriene biosynthetic process / type I pneumocyte differentiation / peptide catabolic process / response to zinc ion / metalloaminopeptidase activity / aminopeptidase activity / lipid metabolic process / response to peptide hormone / tertiary granule lumen / peptidase activity / ficolin-1-rich granule lumen / Neutrophil degranulation / proteolysis / RNA binding / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytosol
Similarity search - Function
Leukotriene A4 hydrolase/leucine aminopeptidase / Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal / Aminopeptidase, leukotriene A4 hydrolase-like / Peptidase M1, LTA-4 hydrolase/aminopeptidase, C-terminal domain superfamily / Leukotriene A4 hydrolase, C-terminal / Leukotriene A4 hydrolase, C-terminal / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain ...Leukotriene A4 hydrolase/leucine aminopeptidase / Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal / Aminopeptidase, leukotriene A4 hydrolase-like / Peptidase M1, LTA-4 hydrolase/aminopeptidase, C-terminal domain superfamily / Leukotriene A4 hydrolase, C-terminal / Leukotriene A4 hydrolase, C-terminal / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Armadillo-type fold
Similarity search - Domain/homology
ACETATE ION / IMIDAZOLE / (4-phenoxyphenyl)methanol / YTTERBIUM (III) ION / Leukotriene A-4 hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSrinivas, H.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Discovery of LYS006, a Potent and Highly Selective Inhibitor of Leukotriene A 4 Hydrolase.
Authors: Markert, C. / Thoma, G. / Srinivas, H. / Bollbuck, B. / Luond, R.M. / Miltz, W. / Walchli, R. / Wolf, R. / Hinrichs, J. / Bergsdorf, C. / Azzaoui, K. / Penno, C.A. / Klein, K. / Wack, N. / ...Authors: Markert, C. / Thoma, G. / Srinivas, H. / Bollbuck, B. / Luond, R.M. / Miltz, W. / Walchli, R. / Wolf, R. / Hinrichs, J. / Bergsdorf, C. / Azzaoui, K. / Penno, C.A. / Klein, K. / Wack, N. / Jager, P. / Hasler, F. / Beerli, C. / Loetscher, P. / Dawson, J. / Wieczorek, G. / Numao, S. / Littlewood-Evans, A. / Rohn, T.A.
History
DepositionNov 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 10, 2021Group: 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 1.4Jan 31, 2024Group: 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: Leukotriene A-4 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2538
Polymers69,4441
Non-polymers8097
Water11,548641
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-38 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.818, 87.025, 98.888
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Leukotriene A-4 hydrolase / LTA-4 hydrolase / Leukotriene A(4) hydrolase


Mass: 69443.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P09960, leukotriene-A4 hydrolase

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Non-polymers , 6 types, 648 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Yb
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-RZN / (4-phenoxyphenyl)methanol


Mass: 200.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 8000, 0.1 IMIDAZOLE PH 6.8, 0.1 SODIUM ACETATE, 0.005 M YBCL3

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→24.89 Å / Num. obs: 49278 / % possible obs: 99.3 % / Redundancy: 5.522 % / Biso Wilson estimate: 22.58 Å2 / Rmerge F obs: 0.142 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.133 / Χ2: 0.968 / Net I/σ(I): 11.85 / Num. measured all: 272119 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.95-25.530.6490.7542.6820024364436210.83399.4
2-2.065.4230.5130.6243.3118877349834810.68999.5
2.06-2.125.3340.4330.5054.1318168343534060.55999.2
2.12-2.185.2670.3490.4254.8717528335033280.4799.3
2.18-2.255.6230.2630.3426.0118234324732430.37699.9
2.25-2.335.7520.2210.2976.9317935312731180.32599.7
2.33-2.425.7340.1810.2527.9617408304630360.27699.7
2.42-2.525.7150.1650.2248.6116580291929010.24699.4
2.52-2.635.5940.1420.189.9215591280227870.19899.5
2.63-2.765.2920.1180.14911.1414097268626640.16499.2
2.76-2.915.5070.0950.12513.1914066256225540.13799.7
2.91-3.085.8220.0730.10415.4314084242824190.11499.6
3.08-3.35.730.0610.08318.4313116229522890.09199.7
3.3-3.565.6550.0480.06721.5312062214521330.07499.4
3.56-3.95.2660.040.05324.110295197719550.05998.9
3.9-4.365.2430.0330.04826.199348179917830.05499.1
4.36-5.035.6640.0280.04429.68971159115840.04899.6
5.03-6.175.4590.0330.05126.697380137313520.05798.5
6.17-8.724.9640.030.04527.685197107610470.0597.3
8.72-24.895.4730.0210.03734.4531586415770.04190

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6end

6end


Resolution: 1.95→24.89 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.9239 / SU R Cruickshank DPI: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.154 / SU Rfree Blow DPI: 0.141 / SU Rfree Cruickshank DPI: 0.136
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 2464 5 %RANDOM
Rwork0.1611 ---
obs0.1634 49277 99.33 %-
Displacement parametersBiso max: 105.96 Å2 / Biso mean: 23.78 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--2.8344 Å20 Å20 Å2
2--5.9307 Å20 Å2
3----3.0963 Å2
Refine analyzeLuzzati coordinate error obs: 0.194 Å
Refinement stepCycle: final / Resolution: 1.95→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4846 0 32 641 5519
Biso mean--33.3 35.63 -
Num. residues----607
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1711SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes120HARMONIC2
X-RAY DIFFRACTIONt_gen_planes724HARMONIC5
X-RAY DIFFRACTIONt_it5007HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion649SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6228SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5007HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6804HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion16.28
LS refinement shellResolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3494 181 5 %
Rwork0.2582 3436 -
all0.2627 3617 -
obs--99.33 %
Refinement TLS params.Method: refined / Origin x: -34.5965 Å / Origin y: 3.663 Å / Origin z: 0.166 Å
111213212223313233
T-0.0271 Å20.0081 Å2-0.0042 Å2--0.04 Å20.0009 Å2---0.041 Å2
L0.2898 °20.0687 °20.0099 °2-0.5926 °20.0429 °2--0.1901 °2
S-0.0099 Å °-0.0137 Å °-0.0107 Å °0.0691 Å °0.0068 Å °-0.0612 Å °0.0267 Å °0.0097 Å °0.0032 Å °
Refinement TLS groupSelection details: { A|* }

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