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- PDB-3chp: Crystal structure of leukotriene a4 hydrolase in complex with (3S... -

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Entry
Database: PDB / ID: 3chp
TitleCrystal structure of leukotriene a4 hydrolase in complex with (3S)-3-amino-4-oxo-4-[(4-phenylmethoxyphenyl)amino]butanoic acid
ComponentsLeukotriene A-4 hydrolase
KeywordsHYDROLASE / EPOXIDE HYDROLASE / ALPHA-BETA PROTEIN / LEUKOTRIENE BIOSYNTHESIS / METALLOPROTEASE / Inhibitor complex / Alternative splicing / Cytoplasm / Metal-binding / Multifunctional enzyme / Zinc
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
Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-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 / Zincin-like - #30 / Zincin-like ...Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-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 / Zincin-like - #30 / Zincin-like / tricorn interacting facor f3 domain / 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 / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4BO / ACETATE ION / IMIDAZOLE / YTTERBIUM (III) ION / Leukotriene A-4 hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å
AuthorsThunnissen, M.M.G.M. / Adler, M. / Whitlow, M.
Citation
Journal: Bioorg.Med.Chem. / Year: 2008
Title: Synthesis of glutamic acid analogs as potent inhibitors of leukotriene A4 hydrolase.
Authors: Kirkland, T.A. / Adler, M. / Bauman, J.G. / Chen, M. / Haeggstrom, J.Z. / King, B. / Kochanny, M.J. / Liang, A.M. / Mendoza, L. / Phillips, G.B. / Thunnissen, M. / Trinh, L. / Whitlow, M. / ...Authors: Kirkland, T.A. / Adler, M. / Bauman, J.G. / Chen, M. / Haeggstrom, J.Z. / King, B. / Kochanny, M.J. / Liang, A.M. / Mendoza, L. / Phillips, G.B. / Thunnissen, M. / Trinh, L. / Whitlow, M. / Ye, B. / Ye, H. / Parkinson, J. / Guilford, W.J.
#1: Journal: Nat.Struct.Biol. / Year: 2001
Title: Crystal Structure of Human Leukotriene A4 Hydrolase, a Bifunctional Enzyme in Inflammation
Authors: Thunnissen, M.M.G.M. / Nordlund, P.N. / Haeggstrom, J.Z.
#2: Journal: FASEB J. / Year: 2002
Title: Crystal structures of LEUKOTRIENE A4 HYDROLASE in complex with captopril and two competitive tight-binding inhibitors.
Authors: Thunnissen, M.M.G.M. / Anderson, B. / Samuelsson, B. / Wong, C.-H. / Haeggstrom, J.Z.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Leukotriene A4 Hydrolase: Selective Abrogation of Leukotriene B4 Formation by Mutation of Aspartic Acid 375.
Authors: Rudberg, P.C. / Tholander, F. / Thunnissen, M.M. / Samuelsson, B. / Haeggstrom, J.Z.
#4: Journal: J.Mol.Biol. / Year: 2004
Title: Leukotriene A4 Hydrolase: Identification of a Common Carboxylate Recognition Site for the Epoxide Hydrolase and Aminopeptidase Substrates
Authors: Rudberg, P.C. / Tholander, F.O.T. / Andberg, M. / Thunnissen, M.M.G.M. / Haeggstrom, J.Z.
History
DepositionMar 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Feb 21, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leukotriene A-4 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9146
Polymers69,2331
Non-polymers6815
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.767, 133.572, 83.629
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1406-

HOH

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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: 69232.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTA4H, LTA4 / Plasmid: PT3-MB4 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P09960, leukotriene-A4 hydrolase

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Non-polymers , 6 types, 241 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Yb
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-4BO / (3S)-3-amino-4-oxo-4-[(4-phenylmethoxyphenyl)amino]butanoic acid


Mass: 314.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N2O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 8
Details: PEG 8000, SODIUM ACETATE, IMIDEAZOLE PH 6.8, YBCL2, BESTATIN, LIQUID DIFFUSION, TEMPERATURE 298K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.007 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 2.1→26.09 Å / Num. obs: 45016 / % possible obs: 99.8 % / Redundancy: 4 % / Biso Wilson estimate: 21.7 Å2 / Rsym value: 0.051 / Net I/σ(I): 11
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 5734 / Rsym value: 0.296 / % possible all: 99.6

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Processing

Software
NameClassification
CNXrefinement
MOSFLMdata reduction
SCALAdata scaling
CNXphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.1→24.85 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2018787.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: THERE IS POSITIVE FO-FC DENSITY BETWEEN THE ZN ION AND THE CARBOXYL OF THE INHIBITOR, AND AT THE 3 POSITION OF THE PHENYL-METHYL AT THE OTHER END OF THE INHIBITOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2248 5.1 %RANDOM
Rwork0.232 ---
all0.24 ---
obs-44475 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.3595 Å2 / ksol: 0.342296 e/Å3
Displacement parametersBiso mean: 39.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--3.16 Å20 Å2
3----4.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4861 0 34 236 5131
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.782
X-RAY DIFFRACTIONc_mcangle_it2.562.05
X-RAY DIFFRACTIONc_scbond_it2.672.5
X-RAY DIFFRACTIONc_scangle_it3.573.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.1-2.170.28992090.26590.02405197.3
2.17-2.260.2932090.25924157
2.26-2.360.31952080.25834130
2.36-2.490.27152220.24064176
2.49-2.640.32442470.25524153
2.64-2.850.3182170.23754224
2.85-3.130.28732320.24844236
3.13-3.590.30961980.24614305
3.59-4.510.25962200.2084356
4.51-24.850.23722854.90.207641044439
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4ZN.parZN.top
X-RAY DIFFRACTION5346.par346.top
X-RAY DIFFRACTION6IMD.parIMD.top
X-RAY DIFFRACTION7ACE.parACE.top

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