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- PDB-3chs: Crystal structure of leukotriene A4 hydrolase in complex with (2S... -

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Database: PDB / ID: 3chs
TitleCrystal structure of leukotriene A4 hydrolase in complex with (2S)-2-amino-5-[[4-[(2S)-2-hydroxy-2-phenyl-ethoxy]phenyl]amino]-5-oxo-pentanoic 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 / 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 / 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 / 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-4BU / IMIDAZOLE / YTTERBIUM (III) ION / Leukotriene A-4 hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.55 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)70,2457
Polymers69,2331
Non-polymers1,0126
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.618, 133.266, 83.644
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-1010-

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, 73 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.: 3 / 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-4BU / (2S)-2-amino-5-[[4-[(2S)-2-hydroxy-2-phenyl-ethoxy]phenyl]amino]-5-oxo-pentanoic acid


Mass: 358.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N2O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 8
Details: PEG 8000, SODIUM ACETATE, IMIDEAZOLE PH 6.8, YBCL2, BESTATIN, PH 8.0, 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
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.55→19.96 Å / Num. all: 25287 / Num. obs: 25287 / % possible obs: 99.98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CNXrefinement
CNXphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.55→19.96 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.814 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.605 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24753 1291 5.1 %RANDOM
Rwork0.21119 ---
obs0.21306 23992 99.98 %-
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: 29.509 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20 Å2
2--2.18 Å20 Å2
3----2.94 Å2
Refinement stepCycle: LAST / Resolution: 2.55→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4876 0 35 67 4978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0215033
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.966838
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6195609
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_restr0.0710.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023794
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.22290
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2192
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0810.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.215
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3371.53054
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.63124962
X-RAY DIFFRACTIONr_scbond_it0.88731979
X-RAY DIFFRACTIONr_scangle_it1.4644.51876
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 (%)
2.55-2.620.331120.2561734100
2.62-2.690.31940.241646100
2.69-2.760.26810.241653100
2.76-2.850.35860.24157799.94
2.85-2.940.33730.231539100
2.94-3.040.27790.23149299.94
3.04-3.150.35870.241432100
3.15-3.270.28770.231417100
3.27-3.420.26810.231338100
3.42-3.580.3680.211291100
3.58-3.760.21620.21231100
3.76-3.980.24570.21204100
3.98-4.250.26690.21106899.91
4.25-4.570.2470.191040100
4.57-4.980.18450.18976100
4.98-5.530.19530.19878100
5.53-6.30.3420.22800100
6.3-7.540.24310.2704100
7.54-9.980.14280.1656799.83
9.98-200.12190.211734405100

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