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- PDB-5aen: Structure of human Leukotriene A4 hydrolase in complex with inhib... -

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Basic information

Entry
Database: PDB / ID: 5aen
TitleStructure of human Leukotriene A4 hydrolase in complex with inhibitor dimethyl(2- (4-phenoxyphenoxy)ethyl)amine
ComponentsLEUKOTRIENE A-4 HYDROLASE
KeywordsHYDROLASE / LEUKOTRIENE (LT) A4 HYDROLASE/AMINOPEPTIDASE / LTA4H
Function / homology
Function and homology information


leukotriene-A4 hydrolase / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase / tripeptide aminopeptidase 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 / leukotriene-A4 hydrolase activity / tripeptide aminopeptidase / tripeptide aminopeptidase 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 / leukotriene biosynthetic process / epoxide hydrolase activity / type I pneumocyte differentiation / response to zinc ion / peptide catabolic process / 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 / 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
N,N-dimethyl-2-(4-phenoxyphenoxy)ethanamine / IMIDAZOLE / YTTERBIUM (III) ION / Leukotriene A-4 hydrolase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.864 Å
AuthorsMoser, D. / Wittmann, S.K. / Kramer, J. / Blocher, R. / Achenbach, J. / Pogoryelov, D. / Proschak, E.
CitationJournal: J.Chem.Inf.Model. / Year: 2015
Title: Peng: A Neural Gas-Based Approach for Pharmacophore Elucidation. Method Design, Validation and Virtual Screening for Novel Ligands of Lta4H.
Authors: Moser, D. / Wittmann, S.K. / Kramer, J. / Blocher, R. / Achenbach, J. / Pogoryelov, D. / Proschak, E.
History
DepositionJan 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Feb 27, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _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: LEUKOTRIENE A-4 HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1609
Polymers69,0071
Non-polymers1,1538
Water10,953608
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.996, 86.953, 98.223
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 LEUKOTRIENE A-4 HYDROLASE / LTA-4 HYDROLASE / LEUKOTRIENE A4 HYDROLASE / LEUKOTRIENE A(4)


Mass: 69006.547 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, 616 molecules

#2: Chemical ChemComp-DP8 / N,N-dimethyl-2-(4-phenoxyphenoxy)ethanamine


Mass: 257.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19NO2
#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 / Ytterbium


Mass: 173.040 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Yb
#5: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 608 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: 1 MICROLITTER OF PROTEIN SOLUTION CONTAINING 10MM TRIS-HCL, 25MM KCL, AND 4 MG/ML TO 8 MG/ML LTA4H (PH 8) WAS MIXED AT DIFFERENT RATIOS (0.5:1, 1:1, AND 1:2) WITH PRECIPITATE SOLUTION ...Details: 1 MICROLITTER OF PROTEIN SOLUTION CONTAINING 10MM TRIS-HCL, 25MM KCL, AND 4 MG/ML TO 8 MG/ML LTA4H (PH 8) WAS MIXED AT DIFFERENT RATIOS (0.5:1, 1:1, AND 1:2) WITH PRECIPITATE SOLUTION CONTAINING 0:15M IMIDAZOLE, 0:1M SODIUM ACETATE PH 6, 14% PEG-8000, AND 5MM YBCL3, AND CRYSTALLIZED AT 17:4 C FOR TWO WEEKS BY HANGING DROP VAPOR-DIFFUSION METHOD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.72873
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.72873 Å / Relative weight: 1
ReflectionResolution: 1.86→49.72 Å / Num. obs: 53242 / % possible obs: 95.6 % / Observed criterion σ(I): 3 / Redundancy: 11.1 % / Biso Wilson estimate: 13.48 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.6
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.3 / % possible all: 63.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GW6

1gw6


Resolution: 1.864→49.715 Å / SU ML: 0.12 / σ(F): 1.32 / Phase error: 18.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1888 4958 5 %
Rwork0.1704 --
obs0.1713 53240 93.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.8 Å2
Refinement stepCycle: LAST / Resolution: 1.864→49.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4854 0 34 608 5496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115008
X-RAY DIFFRACTIONf_angle_d1.2456802
X-RAY DIFFRACTIONf_dihedral_angle_d14.1921840
X-RAY DIFFRACTIONf_chiral_restr0.073756
X-RAY DIFFRACTIONf_plane_restr0.007865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.864-1.88520.3154390.2436716X-RAY DIFFRACTION21
1.8852-1.90740.2751750.22481559X-RAY DIFFRACTION47
1.9074-1.93060.24651140.21272226X-RAY DIFFRACTION65
1.9306-1.95510.22841450.20112741X-RAY DIFFRACTION82
1.9551-1.98080.26251560.19733004X-RAY DIFFRACTION88
1.9808-2.00790.21261670.18133139X-RAY DIFFRACTION94
2.0079-2.03660.23871710.17483261X-RAY DIFFRACTION98
2.0366-2.0670.18661760.16483332X-RAY DIFFRACTION99
2.067-2.09930.18761770.16673351X-RAY DIFFRACTION100
2.0993-2.13370.20131750.16483397X-RAY DIFFRACTION100
2.1337-2.17050.20871760.16013349X-RAY DIFFRACTION100
2.1705-2.210.18681830.15643378X-RAY DIFFRACTION100
2.21-2.25250.18771770.15883342X-RAY DIFFRACTION100
2.2525-2.29850.18331800.16023392X-RAY DIFFRACTION100
2.2985-2.34840.17581820.15653380X-RAY DIFFRACTION100
2.3484-2.40310.19661740.15073384X-RAY DIFFRACTION100
2.4031-2.46320.16981790.15753355X-RAY DIFFRACTION100
2.4632-2.52980.19341780.16333347X-RAY DIFFRACTION100
2.5298-2.60420.17771760.16093349X-RAY DIFFRACTION100
2.6042-2.68820.19081810.16143337X-RAY DIFFRACTION100
2.6882-2.78430.19891800.16713405X-RAY DIFFRACTION100
2.7843-2.89580.20391800.16923377X-RAY DIFFRACTION100
2.8958-3.02760.1811780.18423336X-RAY DIFFRACTION100
3.0276-3.18720.17961790.19083378X-RAY DIFFRACTION100
3.1872-3.38680.1971750.18923383X-RAY DIFFRACTION100
3.3868-3.64820.19431750.17293368X-RAY DIFFRACTION100
3.6482-4.01520.16021760.1613359X-RAY DIFFRACTION100
4.0152-4.59590.15921760.15023373X-RAY DIFFRACTION100
4.5959-5.78890.19371760.16123372X-RAY DIFFRACTION100
5.7889-49.73310.16321820.19253355X-RAY DIFFRACTION100

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