[English] 日本語
Yorodumi
- PDB-2wea: ACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wea
TitleACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PHOSPHONATE INHIBITOR: METHYL[CYCLO-7[(2R)-((N-VALYL) AMINO)-2-(HYDROXYL-(1S)-1-METHYOXYCARBONYL-2-PHENYLETHOXY) PHOSPHINYLOXY-ETHYL]-1-NAPHTHALENEACETAMIDE], SODIUM SALT
ComponentsPENICILLOPEPSIN
KeywordsHYDROLASE / PENICILLOPEPSIN / PHOSPHONATE INHIBITOR
Function / homology
Function and homology information


penicillopepsin / aspartic-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Aspergillopepsin-like catalytic domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Aspergillopepsin-like catalytic domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Chem-PP6 / Penicillopepsin-1
Similarity search - Component
Biological speciesPenicillium janthinellum (fungus)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER METHOD / Resolution: 1.25 Å
AuthorsDing, J. / Fraser, M.E. / James, M.N.G.
Citation
Journal: J.Am.Chem.Soc. / Year: 1998
Title: Macrocyclic Inhibitors of Penicillopepsin. II. X-Ray Crystallographic Analyses of Penicillopepsin Complexed with a P3-P1 Macrocyclic Peptidyl Inhibitor and with its Two Acyclic Analogues
Authors: Ding, J. / Fraser, M.E. / Meyer, J.H. / Bartlett, P.A. / James, M.N.G.
#1: Journal: To be Published
Title: Macrocyclic Inhibitors of Penicillopepsin. I. Design, Synthesis, and Evaluation of an Inhibitor Bridged between P1 and P3
Authors: Meyer, J.H. / Bartlett, P.A.
#2: Journal: Biochemistry / Year: 1992
Title: Crystallographic Analysis of Transition-State Mimics Bound to Penicillopepsin: Phosphorus-Containing Peptide Analogues
Authors: Fraser, M.E. / Strynadka, N.C. / Bartlett, P.A. / Hanson, J.E. / James, M.N.
#3: Journal: Biochemistry / Year: 1992
Title: Crystallographic Analysis of Transition State Mimics Bound to Penicillopepsin: Difluorostatine-and Difluorostatone-Containing Peptides
Authors: James, M.N. / Sielecki, A.R. / Hayakawa, K. / Gelb, M.H.
History
DepositionFeb 3, 1998Processing site: BNL
SupersessionMay 27, 1998ID: 1WEA
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PENICILLOPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4775
Polymers33,4691
Non-polymers1,0084
Water9,224512
1
A: PENICILLOPEPSIN
hetero molecules

A: PENICILLOPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,95310
Polymers66,9382
Non-polymers2,0168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)96.330, 46.270, 64.590
Angle α, β, γ (deg.)90.00, 115.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-863-

HOH

-
Components

#1: Protein PENICILLOPEPSIN


Mass: 33468.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Penicillium janthinellum (fungus) / References: UniProt: P00798, penicillopepsin
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PP6 / METHYL[CYCLO-7[(2R)-((N-VALYL)AMINO)-2-(HYDROXYL-(1S)-1-METHYLOXYCARBONYL-2-PHENYLETHOXY)PHOSPHINYLOXY-ETHYL]-1-NAPHTHALENEACETAMIDE]


Mass: 551.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H32N2O7P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.81 %
Crystal growpH: 4.4 / Details: 0.1M NAC2H3O2 PH=4.4 35-40% SATURATED (NH4)2SO4
Crystal grow
*PLUS
Temperature: 18-22 ℃ / Method: vapor diffusion, hanging drop
Details: used macroseeding, Fraser, M.E., (1992) Biochemistry, 31, 5201.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
134-40 %satammonium sulfate1drop
20.1 M1dropNaC2H3O2
310 mg/mlcomplex1drop

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Mar 22, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.25→40 Å / Num. obs: 58629 / % possible obs: 82.22 % / Observed criterion σ(I): 0 / Redundancy: 3.47 % / Biso Wilson estimate: 10.427 Å2 / Rmerge(I) obs: 0.0595 / Net I/σ(I): 41.28
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 2.05 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 5.18 / % possible all: 40.47
Reflection
*PLUS
Observed criterion σ(I): 2 / Num. measured all: 203415
Reflection shell
*PLUS
% possible obs: 40.47 %

-
Processing

Software
NameClassification
XENGENdata collection
XENGENdata reduction
X-PLORmodel building
TNTrefinement
X-PLORrefinement
XENGENdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER METHOD / Resolution: 1.25→40 Å
Isotropic thermal model: CSDX_PROTGEO.DAT, OTHERGEO.DAT, CPPP6GEO.DAT, SEMTHMGEO.DAT
σ(F): 2
Stereochemistry target values: CSDX_PROTGEO.DAT, OTHERGEO.DAT, CPPP6GEO.DAT, SEMTHMGEO.DAT, CONTACT.DAT
Details: X-PLOR AND TNT ESD FROM SIGMAA (A) : 0.138904 UNCERTAINTY IN RMS ERROR SQUARED : 0.001516
RfactorNum. reflection% reflection
Rfree0.19 -10 %
Rwork0.145 --
obs0.149 55829 78 %
all-58629 -
Solvent computationSolvent model: TNT / Bsol: 441.6 Å2 / ksol: 1.002 e/Å3
Refinement stepCycle: LAST / Resolution: 1.25→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 66 512 2954
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01425011.1
X-RAY DIFFRACTIONt_angle_deg1.45433921.1
X-RAY DIFFRACTIONt_dihedral_angle_d15.71214085
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.016682
X-RAY DIFFRACTIONt_gen_planes0.0263663
X-RAY DIFFRACTIONt_it1.3725010.75
X-RAY DIFFRACTIONt_nbd0.03599
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.155 / Rfactor Rfree: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0162
X-RAY DIFFRACTIONt_plane_restr0.0263

+
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