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- PDB-3b7r: Leukotriene A4 Hydrolase Complexed with Inhibitor RB3040 -

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Basic information

Entry
Database: PDB / ID: 3b7r
TitleLeukotriene A4 Hydrolase Complexed with Inhibitor RB3040
ComponentsLeukotriene A-4 hydrolase
KeywordsHYDROLASE / TRANSITION STATE / ANALOGUE PEPTIDE / HYDROLYSIS / ALTERNATIVE SPLICING / CYTOPLASM / LEUKOTRIENE BIOSYNTHESIS / METAL-BINDING / METALLOPROTEASE / MULTIFUNCTIONAL ENZYME / PROTEASE / ZINC
Function / homology
Function and homology information


leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase activity / tripeptide aminopeptidase / Biosynthesis of protectins / protein metabolic process / 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 ...leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase activity / tripeptide aminopeptidase / Biosynthesis of protectins / protein metabolic process / 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) / epoxide hydrolase activity / leukotriene biosynthetic process / response to zinc ion / peptide catabolic process / type I pneumocyte differentiation / metalloaminopeptidase activity / aminopeptidase activity / response to peptide hormone / lipid metabolic process / tertiary granule lumen / peptidase activity / ficolin-1-rich granule lumen / Neutrophil degranulation / proteolysis / RNA binding / extracellular exosome / extracellular region / zinc ion binding / 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 / Peptidase M1, LTA-4 hydrolase/aminopeptidase, C-terminal domain superfamily / : / Leukotriene A4 hydrolase, C-terminal / Leukotriene A4 hydrolase, C-terminal / Aminopeptidase, leukotriene A4 hydrolase-like / 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 / Peptidase M1, LTA-4 hydrolase/aminopeptidase, C-terminal domain superfamily / : / Leukotriene A4 hydrolase, C-terminal / Leukotriene A4 hydrolase, C-terminal / Aminopeptidase, leukotriene A4 hydrolase-like / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-BIR / IMIDAZOLE / YTTERBIUM (III) ION / Leukotriene A-4 hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.811 Å
AuthorsTholander, F. / Haeggstrom, J. / Thunnissen, M. / Muroya, A. / Roques, B.-P. / Fournie-Zaluski, M.-C.
Citation
Journal: Chem.Biol. / Year: 2008
Title: Structure-based dissection of the active site chemistry of leukotriene a4 hydrolase: implications for m1 aminopeptidases and inhibitor design.
Authors: Tholander, F. / Muroya, A. / Roques, B.P. / Fournie-Zaluski, M.C. / Thunnissen, M.M. / Haeggstrom, J.Z.
#1: Journal: Proteins / Year: 2007
Title: Assay for rapid analysis of the tri-peptidase activity of LTA4 hydrolase.
Authors: Tholander, F. / Haeggstrom, J.Z.
#2: Journal: J.Biol.Chem. / 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. / Andberg, M. / Thunnissen, M.M. / Haeggstrom, J.Z.
#3: Journal: J.Biol.Chem. / Year: 2002
Title: Leukotriene A4 hydrolase/aminopeptidase. Glutamate 271 is a catalytic residue with specific roles in two distinct enzyme mechanisms.
Authors: Rudberg, P.C. / Tholander, F. / Thunnissen, M.M. / Haeggstrom, J.Z.
#4: 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.
#5: Journal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure of human leukotriene A(4) hydrolase, a bifunctional enzyme in inflammation.
Authors: Thunnissen, M.M. / Nordlund, P. / Haeggstrom, J.Z.
History
DepositionOct 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 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 1.3Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _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
L: Leukotriene A-4 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7885
Polymers70,0621
Non-polymers7264
Water12,034668
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.330, 86.937, 99.109
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules L

#1: Protein Leukotriene A-4 hydrolase / LTA-4 hydrolase / Leukotriene A4 / hydrolase


Mass: 70061.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTA4H, LTA4 / Plasmid: pT7T3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P09960, leukotriene-A4 hydrolase

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Non-polymers , 5 types, 672 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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-BIR / N-[3-[(1-AMINOETHYL)(HYDROXY)PHOSPHORYL]-2-(1,1'-BIPHENYL-4-YLMETHYL)PROPANOYL]ALANINE


Mass: 418.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N2O5P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / 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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 298 K / Method: liquid-liquid diffusion
Details: CO-CRYSTALLIZED WITH LTA4H BY LIQUID-LIQUID DIFFUSION IN MELTING-POINT CAPILLARIES. A TRIS-BUFFERED (10 mM, PH 7.5) SOLUTION OF PROTEIN AND INHIBITOR IN APPROXIMATELY EQUIMOLAR ...Details: CO-CRYSTALLIZED WITH LTA4H BY LIQUID-LIQUID DIFFUSION IN MELTING-POINT CAPILLARIES. A TRIS-BUFFERED (10 mM, PH 7.5) SOLUTION OF PROTEIN AND INHIBITOR IN APPROXIMATELY EQUIMOLAR CONCENTRATIONS (~70 MICROM) WAS LAYERED ON THE PRECIPITATE SOLUTION CONTAINING 28% (WEIGHT/VOLUME) POLYETHYLENE GLYCOL (MW 8000), 50 mM NA ACETATE, 100 mM IMIDAZOLE, PH 6.8, AND 5 MM YBCL3, liquid-liquid diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 15, 2003
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.811→15.534 Å / Num. obs: 61881 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.811-1.913.90.2552.83379686030.25595.7
1.91-2.024.10.1754.13481985310.175100
2.02-2.164.10.1275.73285180110.127100
2.16-2.344.10.0937.73064274620.093100
2.34-2.564.10.0759.72844869340.075100
2.56-2.864.10.05612.72567362570.056100
2.86-3.34.10.045152280955750.045100
3.3-4.054.10.032191931147420.032100
4.05-5.7240.02621.11498337250.026100
5.72-15.673.80.02718.6779620410.02795.1

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
RefinementStarting model: pdb entry 1H19

1h19


Resolution: 1.811→15.534 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.978 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.185 2050 3.3 %RANDOM
Rwork0.149 ---
obs0.15 59767 99.34 %-
all-61817 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.789 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.61 Å20 Å2
3---0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.811→15.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4877 0 36 668 5581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0215037
X-RAY DIFFRACTIONr_bond_other_d0.0020.024530
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.9616846
X-RAY DIFFRACTIONr_angle_other_deg1.059310600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1495609
X-RAY DIFFRACTIONr_chiral_restr0.110.2765
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025519
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02989
X-RAY DIFFRACTIONr_nbd_refined0.2110.21044
X-RAY DIFFRACTIONr_nbd_other0.250.25320
X-RAY DIFFRACTIONr_nbtor_other0.0860.22775
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2484
X-RAY DIFFRACTIONr_metal_ion_refined0.050.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.320.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4130.228
X-RAY DIFFRACTIONr_mcbond_it0.8881.53055
X-RAY DIFFRACTIONr_mcangle_it1.60424963
X-RAY DIFFRACTIONr_scbond_it2.73331982
X-RAY DIFFRACTIONr_scangle_it4.3694.51883
LS refinement shellResolution: 1.811→1.858 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.195 136
Rwork0.172 4139
all-4275
obs-4139

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