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- PDB-2xe4: Structure of Oligopeptidase B from Leishmania major -

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Basic information

Entry
Database: PDB / ID: 2xe4
TitleStructure of Oligopeptidase B from Leishmania major
Components
  • ANTIPAIN
  • OLIGOPEPTIDASE B
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / HYDROLASE / PROTEASE INHIBITOR TRYPANOSOMES / CLAN SC
Function / homology
Function and homology information


oligopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / cytosol / cytoplasm
Similarity search - Function
: / Prolyl oligopeptidase, N-terminal domain / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller ...: / Prolyl oligopeptidase, N-terminal domain / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Antipain / S-1,2-PROPANEDIOL / R-1,2-PROPANEDIOL / PHOSPHATE ION / : / Prolyl endopeptidase
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
ACTINOBACTERIA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsMcLuskey, K. / Paterson, N.G. / Bland, N.D. / Mottram, J.C. / Isaacs, N.W.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal Structure of Leishmania Major Oligopeptidase B Gives Insight Into the Enzymatic Properties of a Trypanosomatid Virulence Factor.
Authors: Mcluskey, K. / Paterson, N.G. / Bland, N.D. / Isaacs, N.W. / Mottram, J.C.
History
DepositionMay 11, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Aug 7, 2013Group: Other
Revision 2.0May 15, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Polymer sequence
Category: database_PDB_caveat / database_PDB_rev ...database_PDB_caveat / database_PDB_rev / database_PDB_rev_record / diffrn / entity_poly / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / pdbx_validate_polymer_linkage / struct_biol / struct_conn
Item: _diffrn.ambient_temp / _entity_poly.pdbx_seq_one_letter_code_can ..._diffrn.ambient_temp / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id / _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: OLIGOPEPTIDASE B
B: ANTIPAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,97370
Polymers85,8512
Non-polymers5,12268
Water12,989721
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.478, 142.776, 208.919
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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

#1: Protein OLIGOPEPTIDASE B / FAMILY S9A-LIKE PROTEIN / SERINE PEPTIDASE


Mass: 85244.297 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Strain: FRIEDLIN / Plasmid: PBP218 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)(PLYS) / References: UniProt: Q4QHU7, EC: 3.4.21.83
#2: Protein/peptide ANTIPAIN


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 606.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Acts as a reversible inhibitor of serine/cysteine proteases and some trypsin-like serine proteases.
Source: (natural) ACTINOBACTERIA (bacteria) / References: NOR: NOR00664, Antipain

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Non-polymers , 7 types, 789 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C3H8O2
#5: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsANTIPAIN HYDROCHLORIDE IS A REVERSIBLE INHIBITOR OF SERINE/CYSTEINE PROTEASES AND SOME TRYPSIN-LIKE ...ANTIPAIN HYDROCHLORIDE IS A REVERSIBLE INHIBITOR OF SERINE/CYSTEINE PROTEASES AND SOME TRYPSIN-LIKE SERINE PROTEASES. ITS ACTION RESEMBLES LEUPEPTIN; HOWEVER, ITS PLASMIN INHIBITION IS LESS AND ITS CATHEPSIN A INHIBITION IS MORE THAN THAT OBSERVED WITH LEUPEPTIN. IT IS AN INHIBITOR OF TRYPSIN-LIKE PROTEASES (E.G. TRYPSIN, PAPAIN, CATHEPSIN B); CATHEPSIN A, A CARBOXYPEPTIDASE IS INHIBITED TOO, WHICH IS NOT TRUE FOR OTHER INHIBITORS FROM ACTINOMYCES.THE NAME IS DERIVED FROM ANTI-PAPAIN. GROUP: 1 NAME: ANTIPAIN CHAIN: B COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 4 DESCRIPTION: ANTIPAIN FORMS A COVALENT LINKAGE BETWEEN THE ARGINAL RESIDUE OF THE INHIBITOR AND SER RESIDUE OF THE PROTEIN.THE PROTEASE INHIBITOR ANTIPAIN INCREASES THE EFFECTIVENESSOF UV IRRADIATION ON CESSATION OF RESPIRATION AND CELL KILLING IN ESCHERICHIA COLI B/R CULTURES WITHOUT AFFECTING EXCISION OF PYRIMIDINE DIMERS. THE ACTIONS ARE SIMILAR TO THOSE CAUSED BY CYCLIC AMP IN IRRADIATED CULTURES. ENGINEERED RESIDUE IN CHAIN A, PHE 25 TO LEU
Has protein modificationY
Nonpolymer detailsCHLORINE ION (CL): NA

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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: 4.2 Å3/Da / Density % sol: 71 % / Description: NONE
Crystal growpH: 4.2
Details: PROTEIN WAS DIALYZED INTO 50 MM TRIS, PH 8.0 AND INCUBATED WITH 10 MM ANTIPAIN FOR 30 MINS. THIS WAS MIXED IN A 1:1 RATIO WITH 25% 1,2 PROPANEDIOL, 10% GLYCEROL, 5 % PEG300 AND 0.1 M PHOSPHATE CITRATE, PH 4.2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21031
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU MICROMAX-00711.541
SYNCHROTRONESRF BM1421.005
Detector
TypeIDDetectorDateDetails
MARRESEARCH1IMAGE PLATEJun 10, 2008MIRRORS
MARRESEARCH2CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.5411
21.0051
ReflectionResolution: 1.65→32 Å / Num. obs: 167772 / % possible obs: 98.4 % / Observed criterion σ(I): 1.5 / Redundancy: 3.3 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.8
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
d*TREKdata reduction
SCALAdata scaling
autoSHARPphasing
SHELXCDphasing
SHELXDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.65→117.851 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.971 / SU B: 3.558 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-9 AND 731 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.178 8321 5.08 %RANDOM
Rwork0.1403 ---
obs0.142 167169 98.007 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 41.338 Å2
Baniso -1Baniso -2Baniso -3
1-2.673 Å20 Å20 Å2
2---1.71 Å20 Å2
3----0.963 Å2
Refinement stepCycle: LAST / Resolution: 1.65→117.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5809 0 326 721 6856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0226627
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3531.9828977
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6615819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73823.738305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49151084
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5321546
X-RAY DIFFRACTIONr_chiral_restr0.2090.2975
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215027
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.23318
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24107
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2704
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0650.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.291
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8331.53852
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.11826311
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.79432775
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.5124.52648
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.90336627
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 605 -
Rwork0.293 11787 -
obs--98.914 %

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