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- PDB-5fwq: Apo structure of human Leukotriene A4 hydrolase -

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Basic information

Entry
Database: PDB / ID: 5fwq
TitleApo structure of human Leukotriene A4 hydrolase
ComponentsHUMAN LEUKOTRIENE A4 HYDROLASE
KeywordsHYDROLASE / LEUKOTRIENE (LT) A4 HYDROLASE/AMINOPEPTIDASE / LTA4H
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
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, 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 / 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 / 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
ACETATE ION / IMIDAZOLE / YTTERBIUM (III) ION / Leukotriene A-4 hydrolase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.047 Å
AuthorsWittmann, S.K. / Kalinowsky, L. / Kramer, J. / Bloecher, R. / Steinhilber, D. / Pogoryelov, D. / Proschak, E. / Heering, J.
Citation
Journal: Bioorg.Med.Chem. / Year: 2016
Title: Thermodynamic properties of leukotriene A4hydrolase inhibitors.
Authors: Wittmann, S.K. / Kalinowsky, L. / Kramer, J.S. / Bloecher, R. / Knapp, S. / Steinhilber, D. / Pogoryelov, D. / Proschak, E. / Heering, J.
#1: Journal: Bioorg.Med.Chem. / Year: 2016
Title: Thermodynamic Properties of Leukotriene A4 Hydrolase Inhibitors.
Authors: Wittmann, S.K. / Kalinowsky, L. / Kramer, J.S. / Bloecher, R. / Knapp, S. / Steinhilber, D. / Pogoryelov, D. / Proschak, E. / Heering, J.
History
DepositionFeb 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / citation_author ...citation / citation_author / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.ptnr1_symmetry / _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.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.ptnr1_symmetry / _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_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: HUMAN LEUKOTRIENE A4 HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,18712
Polymers71,8171
Non-polymers1,37011
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.337, 86.980, 96.310
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 A

#1: Protein HUMAN LEUKOTRIENE A4 HYDROLASE / LTA-4 HYDROLASE / LEUKOTRIENE A(4) HYDROLASE / HUMAN LEUKOTRIENE A4 HYDROLASE


Mass: 71816.711 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) / Strain (production host): BL21(DE3) / References: UniProt: P09960, leukotriene-A4 hydrolase

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Non-polymers , 5 types, 418 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 173.040 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Yb
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.23 Å3/Da / Density % sol: 44.75 % / Description: NONE
Crystal growTemperature: 290.55 K / Method: vapor diffusion, hanging drop
Details: PROTEIN SOLUTION: 10 MM TRIS-HCL, 25 MM KCL, 4-8 MG/ML PROTEIN (PH8); PRECIPITATE SOLUTION: 0,15M IMIDAZOL/HCL PH6.5; 0,1 M NAACETAT, 14% PEG8000, 5 MM YBCL3 AND 25 MM 5-CHLORO-3- ...Details: PROTEIN SOLUTION: 10 MM TRIS-HCL, 25 MM KCL, 4-8 MG/ML PROTEIN (PH8); PRECIPITATE SOLUTION: 0,15M IMIDAZOL/HCL PH6.5; 0,1 M NAACETAT, 14% PEG8000, 5 MM YBCL3 AND 25 MM 5-CHLORO-3-HYDROXYPYRIDINE; HANGING DROP VAPOR-DIFFUSION AT 290.55 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.05→49.29 Å / Num. obs: 40948 / % possible obs: 99.7 % / Observed criterion σ(I): 1.5 / Redundancy: 13.3 % / Biso Wilson estimate: 20.92 Å2 / Rmerge(I) obs: 0.31 / Net I/σ(I): 7.58
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 1.87 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AEN

5aen


Resolution: 2.047→49.291 Å / SU ML: 0.17 / σ(F): 1.14 / Phase error: 20.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 1374 1.8 %
Rwork0.1934 --
obs0.1939 40948 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.8 Å2
Refinement stepCycle: LAST / Resolution: 2.047→49.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4846 0 26 407 5279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074988
X-RAY DIFFRACTIONf_angle_d1.0086774
X-RAY DIFFRACTIONf_dihedral_angle_d14.1671827
X-RAY DIFFRACTIONf_chiral_restr0.044754
X-RAY DIFFRACTIONf_plane_restr0.004864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0473-2.12050.28591350.24797560X-RAY DIFFRACTION98
2.1205-2.20540.25141380.23567605X-RAY DIFFRACTION100
2.2054-2.30580.26621410.22347655X-RAY DIFFRACTION100
2.3058-2.42730.23831410.20817629X-RAY DIFFRACTION100
2.4273-2.57940.28561370.20917700X-RAY DIFFRACTION100
2.5794-2.77850.25821370.19717642X-RAY DIFFRACTION100
2.7785-3.05810.22431360.19747651X-RAY DIFFRACTION100
3.0581-3.50050.2431320.1847656X-RAY DIFFRACTION100
3.5005-4.40980.20521390.15977660X-RAY DIFFRACTION100
4.4098-49.30510.15381380.18087650X-RAY DIFFRACTION100

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