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- PDB-6enb: LTA4 hydrolase (E297Q) mutant in complex with Pro-Gly-Pro peptide -

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Basic information

Entry
Database: PDB / ID: 6enb
TitleLTA4 hydrolase (E297Q) mutant in complex with Pro-Gly-Pro peptide
Components
  • Leukotriene A-4 hydrolase
  • PRO-GLY-PRO
KeywordsHYDROLASE / LTA4H / Substrate
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
ACETATE ION / IMIDAZOLE / YTTERBIUM (III) ION / Leukotriene A-4 hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsSrinivas, H.
CitationJournal: Sci Rep / Year: 2017
Title: Feasibility and physiological relevance of designing highly potent aminopeptidase-sparing leukotriene A4 hydrolase inhibitors.
Authors: Numao, S. / Hasler, F. / Laguerre, C. / Srinivas, H. / Wack, N. / Jager, P. / Schmid, A. / Osmont, A. / Rothlisberger, P. / Houguenade, J. / Bergsdorf, C. / Dawson, J. / Carte, N. / Hofmann, ...Authors: Numao, S. / Hasler, F. / Laguerre, C. / Srinivas, H. / Wack, N. / Jager, P. / Schmid, A. / Osmont, A. / Rothlisberger, P. / Houguenade, J. / Bergsdorf, C. / Dawson, J. / Carte, N. / Hofmann, A. / Markert, C. / Hardaker, L. / Billich, A. / Wolf, R.M. / Penno, C.A. / Bollbuck, B. / Miltz, W. / Rohn, T.A.
History
DepositionOct 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / entity_src_nat / struct_ref_seq_dif
Item: _entity.pdbx_mutation / _entity.src_method / _struct_ref_seq_dif.details
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_asym_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_asym_id / _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_asym_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_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leukotriene A-4 hydrolase
B: PRO-GLY-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0987
Polymers69,5582
Non-polymers5405
Water12,178676
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-48 kcal/mol
Surface area23870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.443, 87.576, 99.058
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Leukotriene A-4 hydrolase / LTA-4 hydrolase / Leukotriene A(4) hydrolase


Mass: 69288.844 Da / Num. of mol.: 1 / Mutation: E297Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTA4H, LTA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P09960, leukotriene-A4 hydrolase
#2: Protein/peptide PRO-GLY-PRO


Mass: 269.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 681 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Yb
#6: Chemical ChemComp-IMD / IMIDAZOLE


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


Mass: 18.015 Da / Num. of mol.: 676 / 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: 49.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 8000, 0.1 IMIDAZOLE PH 6.8, 0.1 M SODIUM ACETATE, 0.005 M YBCL3

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 59014 / % possible obs: 99.8 % / Redundancy: 6.5 % / Net I/σ(I): 13

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→29.01 Å / Cor.coef. Fo:Fc: 0.9556 / Cor.coef. Fo:Fc free: 0.9481 / SU R Cruickshank DPI: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.12 / SU Rfree Blow DPI: 0.109 / SU Rfree Cruickshank DPI: 0.105
RfactorNum. reflection% reflectionSelection details
Rfree0.1861 2951 5 %RANDOM
Rwork0.1554 ---
obs0.1569 59014 99.85 %-
Displacement parametersBiso max: 99.03 Å2 / Biso mean: 27.05 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--1.0898 Å20 Å20 Å2
2--5.1794 Å20 Å2
3----4.0896 Å2
Refine analyzeLuzzati coordinate error obs: 0.172 Å
Refinement stepCycle: final / Resolution: 1.84→29.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4865 0 31 676 5572
Biso mean--40.56 41.38 -
Num. residues----607
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1710SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes121HARMONIC2
X-RAY DIFFRACTIONt_gen_planes719HARMONIC5
X-RAY DIFFRACTIONt_it5006HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion651SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6162SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5006HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6806HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion15.81
LS refinement shellResolution: 1.84→1.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2686 216 5 %
Rwork0.2089 4108 -
all0.2118 4324 -
obs--99.85 %
Refinement TLS params.Method: refined / Origin x: 4.2957 Å / Origin y: 3.6843 Å / Origin z: 0.1249 Å
111213212223313233
T-0.0218 Å20.0036 Å20.0047 Å2--0.0199 Å2-0.0014 Å2---0.0333 Å2
L0.2291 °20.0238 °20.0312 °2-0.6768 °20.0355 °2--0.1435 °2
S-0.0216 Å °-0.0064 Å °-0.0076 Å °0.0406 Å °0.0182 Å °-0.0449 Å °0.0196 Å °-0.0009 Å °0.0033 Å °
Refinement TLS groupSelection details: { A|* }

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