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- PDB-7av1: LTA4 hydrolase in complex with fragment2 -

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Basic information

Entry
Database: PDB / ID: 7av1
TitleLTA4 hydrolase in complex with fragment2
ComponentsLeukotriene A-4 hydrolase
KeywordsHYDROLASE / inhibitor / complex
Function / homology
Function and homology information


leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase activity / tripeptide aminopeptidase / 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 / protein metabolic process ...leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase activity / tripeptide aminopeptidase / 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 / protein metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / 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 / extracellular exosome / zinc ion binding / 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 / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal 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 / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / 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 / Chem-RZK / YTTERBIUM (III) ION / Leukotriene A-4 hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 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)70,2728
Polymers69,4441
Non-polymers8287
Water14,772820
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 area23690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.873, 87.109, 98.962
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, 827 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-RZK / 2-[5-(4-methoxyphenyl)-1,2,3,4-tetrazol-2-yl]ethanamine


Mass: 219.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 820 / 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: 2.42 Å3/Da / Density % sol: 49.1 %
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: Dec 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→24.18 Å / Num. obs: 63418 / % possible obs: 98.9 % / Redundancy: 5.566 % / Biso Wilson estimate: 20.95 Å2 / Rmerge F obs: 0.113 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.096 / Χ2: 1.01 / Net I/σ(I): 14.19 / Num. measured all: 352987 / Scaling rejects: 4
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
1.79-1.845.5470.6130.6782.6125514468346000.74898.2
1.84-1.895.7950.450.5273.4126102458345040.57998.3
1.89-1.945.7760.3390.4114.3225270444543750.45198.4
1.94-25.7580.2860.3365.2924535431742610.36998.7
2-2.075.7160.2320.2686.4923537418041180.29598.5
2.07-2.145.6560.1930.2197.7822512402539800.24198.9
2.14-2.225.340.1590.1779.0320873394539090.19699.1
2.22-2.315.2560.1350.14510.6919580376737250.16198.9
2.31-2.415.8150.1010.12612.9720946363336020.13999.1
2.41-2.535.8350.0920.11214.3420055346134370.12399.3
2.53-2.675.7530.0750.09516.4518920331432890.10499.2
2.67-2.835.6360.0620.0818.9417539313231120.08899.4
2.83-3.035.4620.0580.07320.6816042295129370.08199.5
3.03-3.275.0360.0510.06123.0813804275527410.06999.5
3.27-3.585.4460.0360.04828.7913854255825440.05399.5
3.58-45.6430.0270.0433.6513023231923080.04499.5
4-4.625.4760.0230.03635.9111270206420580.03999.7
4.62-5.665.1080.0230.03535.458950175517520.03999.8
5.66-8.014.810.0260.03833.376676139213880.04399.7
8.01-24.185.1220.0160.02840.8739858187780.03195.1

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Phasing

PhasingMethod: molecular replacement

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Processing

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

6end


Resolution: 1.79→24.18 Å / Cor.coef. Fo:Fc: 0.9575 / Cor.coef. Fo:Fc free: 0.9446 / SU R Cruickshank DPI: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.116 / SU Rfree Blow DPI: 0.111 / SU Rfree Cruickshank DPI: 0.105
RfactorNum. reflection% reflectionSelection details
Rfree0.1957 3171 5 %RANDOM
Rwork0.1567 ---
obs0.1586 63418 98.99 %-
Displacement parametersBiso max: 103.54 Å2 / Biso mean: 22.41 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-1.6426 Å20 Å20 Å2
2--1.1592 Å20 Å2
3----2.8018 Å2
Refine analyzeLuzzati coordinate error obs: 0.168 Å
Refinement stepCycle: final / Resolution: 1.79→24.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4846 0 33 820 5699
Biso mean--28.47 36.4 -
Num. residues----607
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1712SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes120HARMONIC2
X-RAY DIFFRACTIONt_gen_planes724HARMONIC5
X-RAY DIFFRACTIONt_it5008HARMONIC20
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_contact6399SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5008HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6806HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.66
X-RAY DIFFRACTIONt_other_torsion15.82
LS refinement shellResolution: 1.79→1.84 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2685 229 4.98 %
Rwork0.216 4365 -
all0.2186 4594 -
obs--98.99 %
Refinement TLS params.Method: refined / Origin x: -34.5984 Å / Origin y: 3.7095 Å / Origin z: 0.195 Å
111213212223313233
T-0.024 Å20.0058 Å2-0.0026 Å2--0.0239 Å2-0.0042 Å2---0.0425 Å2
L0.2146 °20.077 °20.0143 °2-0.5143 °20.0329 °2--0.147 °2
S-0.0141 Å °0.0011 Å °-0.0055 Å °0.0312 Å °0.017 Å °-0.0327 Å °0.0211 Å °0.0018 Å °-0.003 Å °
Refinement TLS groupSelection details: { A|* }

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