[English] 日本語
Yorodumi
- PDB-3b7t: [E296Q]LTA4H in complex with Arg-Ala-Arg substrate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b7t
Title[E296Q]LTA4H in complex with Arg-Ala-Arg substrate
Components
  • Leukotriene A-4 hydrolase
  • RAR peptide
KeywordsHYDROLASE / TRANSITION STATE / ANALOGUE PEPTIDE / HYDROLYSIS / ALTERNATIVE SPLICING / CYTOPLASM / LEUKOTRIENE BIOSYNTHESIS / METAL-BINDING / METALLOPROTEASE / MULTIFUNCTIONAL ENZYME / PROTEASE / ZINC / TRIPEPTIDE SUBSTRATE
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
IMIDAZOLE / YTTERBIUM (III) ION / Leukotriene A-4 hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsTholander, F. / Haeggstrom, J. / Thunnissen, M. / Muroya, A. / Roques, B.-P. / Fournie-Zaluski, M.-C.
Citation
Journal: Chem.Biol. / Year: 2008
Title: Structure-based dissection of the active site chemistry of leukotriene a4 hydrolase: implications for m1 aminopeptidases and inhibitor design.
Authors: Tholander, F. / Muroya, A. / Roques, B.P. / Fournie-Zaluski, M.C. / Thunnissen, M.M. / Haeggstrom, J.Z.
#1: Journal: Proteins / Year: 2007
Title: Assay for rapid analysis of the tri-peptidase activity of LTA4 hydrolase.
Authors: Tholander, F. / Haeggstrom, J.Z.
#2: Journal: J.Biol.Chem. / 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. / Andberg, M. / Thunnissen, M.M. / Haeggstrom, J.Z.
#3: Journal: J.Biol.Chem. / Year: 2002
Title: Leukotriene A4 hydrolase/aminopeptidase. Glutamate 271 is a catalytic residue with specific roles in two distinct enzyme mechanisms.
Authors: Rudberg, P.C. / Tholander, F. / Thunnissen, M.M. / Haeggstrom, J.Z.
#4: 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.
#5: Journal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure of human leukotriene A(4) hydrolase, a bifunctional enzyme in inflammation.
Authors: Thunnissen, M.M. / Nordlund, P. / Haeggstrom, J.Z.
History
DepositionOct 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 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 1.3Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_conn_angle / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Leukotriene A-4 hydrolase
B: RAR peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9456
Polymers70,4642
Non-polymers4814
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.490, 87.785, 99.916
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

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

#1: Protein Leukotriene A-4 hydrolase / LTA-4 hydrolase / Leukotriene A(4) hydrolase / Tripeptide aminopeptidase LTA4H


Mass: 70060.664 Da / Num. of mol.: 1 / Mutation: E296Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTA4H, LTA4 / Plasmid: pT7T3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101
References: UniProt: P09960, leukotriene-A4 hydrolase, tripeptide aminopeptidase
#2: Protein/peptide RAR peptide


Mass: 403.481 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Non-polymers , 4 types, 35 molecules

#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.: 2 / Source method: obtained synthetically / Formula: Yb
#5: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


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


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 298 K / Method: liquid-liquid diffusion
Details: TRI-PEPTIDE WAS CO-CRYSTALLIZED WITH [E296Q]LTA4H BY LIQUID-LIQUID DIFFUSION IN MELTING-POINT CAPILLARIES. A TRIS-BUFFERED (10 mM, PH 7.5) SOLUTION OF PROTEIN AND TRIPEPTIDE, MOLAR RATIO 1: ...Details: TRI-PEPTIDE WAS CO-CRYSTALLIZED WITH [E296Q]LTA4H BY LIQUID-LIQUID DIFFUSION IN MELTING-POINT CAPILLARIES. A TRIS-BUFFERED (10 mM, PH 7.5) SOLUTION OF PROTEIN AND TRIPEPTIDE, MOLAR RATIO 1:10 (~70 MICROM PROTEIN), WAS LAYERED ON THE PRECIPITATE SOLUTION CONTAINING 28% (WEIGHT/VOLUME) POLYETHYLENE GLYCOL (MW 8000), 50 mM NA ACETATE, 100 mM IMIDAZOLE, PH 6.8, AND 5 MM YBCL3. CRYSTALS WERE ADDITIONALLY SOAKED IN SOLUTIONS WITH INCREASED TRI-PEPTIDE CONCENTRATION PRIOR TO DATA COLLECTION, liquid-liquid diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 5, 2005
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→43.42 Å / Num. all: 57197 / Num. obs: 57220 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.1 Å2 / Limit h max: 34 / Limit h min: 0 / Limit k max: 37 / Limit k min: 0 / Limit l max: 43 / Limit l min: -43 / Observed criterion F max: 2242927.86 / Observed criterion F min: 13.9 / Rmerge(I) obs: 0.125 / Net I/σ(I): 7.45
Reflection shellResolution: 2.3→2.5 Å / Redundancy: 2.54 % / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 2.8 / Num. measured obs: 32893 / Num. unique all: 3665 / Num. unique obs: 12804 / % possible all: 97.7

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
XFITdata reduction
RefinementStarting model: pdb entry 1H19

1h19


Resolution: 2.3→30 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.792 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1902 3.3 %RANDOM
Rwork0.206 ---
all-59235 --
obs-57183 96.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 42.0763 Å2 / ksol: 0.379436 e/Å3
Displacement parametersBiso max: 180.76 Å2 / Biso mean: 49.7 Å2 / Biso min: 20.13 Å2
Baniso -1Baniso -2Baniso -3
1-4.92 Å20 Å20 Å2
2---5.86 Å20 Å2
3---0.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.37 Å
Luzzati d res high-2.3
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4903 0 8 31 4942
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg22.7
X-RAY DIFFRACTIONx_torsion_impr_deg0.85
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.3-2.40.3392543.50.29469600.0217401721497.5
2.4-2.530.3912433.30.30370190.0257447726297.5
2.53-2.690.3352343.20.27569960.0227407723097.6
2.69-2.90.2742273.10.24670400.0187424726797.9
2.9-3.190.3042623.60.24269170.0197381717997.3
3.19-3.650.2642233.10.19669310.0187413715496.5
3.65-4.590.2422403.40.17567550.0167410699594.4
4.59-29.260.2432193.20.18166630.0167413688292.8

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more