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- PDB-3chr: Crystal structure of leukotriene A4 hydrolase in complex with 4-a... -

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Entry
Database: PDB / ID: 3chr
TitleCrystal structure of leukotriene A4 hydrolase in complex with 4-amino-N-[4-(phenylmethoxy)phenyl]-butanamide
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
4-amino-N-[4-(benzyloxy)phenyl]butanamide / IMIDAZOLE / YTTERBIUM (III) ION / Leukotriene A-4 hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 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 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Leukotriene A-4 hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8255
Polymers69,2331
Non-polymers5924
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.346, 133.210, 83.100
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-642-

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 , 5 types, 364 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-4BS / 4-amino-N-[4-(benzyloxy)phenyl]butanamide


Mass: 284.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N2O2
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.69 Å3/Da / Density % sol: 54.31 %
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: 1.091 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.091 Å / Relative weight: 1
ReflectionResolution: 2.2→17.68 Å / Num. obs: 38521 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.071 / Net I/σ(I): 6.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 5572 / Rsym value: 0.328 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CNXrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.2→17.62 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.496 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.268 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26694 1704 4.4 %RANDOM
Rwork0.20682 ---
obs0.20948 36768 99.59 %-
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: 36.305 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--1.15 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.2→17.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4877 0 28 360 5265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0215029
X-RAY DIFFRACTIONr_bond_other_d0.0020.024510
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9596831
X-RAY DIFFRACTIONr_angle_other_deg0.851310543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5015609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025522
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021004
X-RAY DIFFRACTIONr_nbd_refined0.2130.21168
X-RAY DIFFRACTIONr_nbd_other0.2310.25378
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.22762
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2336
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1240.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3850.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3750.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7111.53055
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29324963
X-RAY DIFFRACTIONr_scbond_it1.72631974
X-RAY DIFFRACTIONr_scangle_it2.7734.51868
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2-2.260.3241420.247263699.78
2.26-2.320.311060.242589100
2.32-2.380.321180.23252499.92
2.38-2.460.311130.222445100
2.46-2.530.291030.23238599.96
2.53-2.620.33940.232336100
2.62-2.720.281140.22221699.96
2.72-2.830.281120.222136100
2.83-2.950.291000.23206499.95
2.95-3.090.3860.23199899.86
3.09-3.250.291070.22185399.69
3.25-3.440.26800.22180299.47
3.44-3.670.26840.2167899.32
3.67-3.950.24660.2160499.11
3.95-4.30.24650.19145899.09
4.3-4.770.2460.18136199.36
4.77-5.450.23380.18121998.43
5.45-6.510.26510.18103998.64
6.51-8.640.17450.1784597.91
8.64-17.620.24340.19263658096.39

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