[English] 日本語
Yorodumi
- PDB-1ppm: CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PEN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ppm
TitleCRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHORUS-CONTAINING PEPTIDE ANALOGUES
ComponentsPENICILLOPEPSIN
KeywordsHYDROLASE/hydrolase inhibitor / ACID PROTEINASE / HYDROLASE-hydrolase inhibitor complex
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
Cbz-Ala-Ala-Leu(P)-(O)-Phe-OMe / Chem-0P1 / alpha-L-arabinopyranose / alpha-D-mannopyranose / Penicillopepsin-1
Similarity search - Component
Biological speciesPenicillium janthinellum (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsFraser, M.E. / James, M.N.G.
Citation
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.
#1: Journal: Biological Macromolecules and Assemblies / Year: 1987
Title: Aspartic Proteinases and Their Catalytic Pathway
Authors: James, M.N.G. / Sielecki, A.R.
#2: Journal: Biochemistry / Year: 1985
Title: Stereochemical Analysis of Peptide Bond Hydrolysis Catalyzed by the Aspartic Proteinase Penicillopepsin
Authors: James, M.N.G. / Sielecki, A.R.
#3: Journal: J.Mol.Biol. / Year: 1983
Title: Structure and Refinement of Penicillopepsin at 1.8 Angstroms Resolution
Authors: James, M.N.G. / Sielecki, A.R.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Conformational Flexibility in the Active Sites of Aspartyl Proteinases Revealed by a Pepstatin Fragment Binding to Penicillopepsin
Authors: James, M.N.G. / Sielecki, A. / Salituro, F. / Rich, D.H. / Hofmann, T.
#5: Journal: STRUCTURAL STUDIES ON MOLECULES OF BIOLOGICA INTERESTL
Year: 1981
Title: The Tertiary Structure of Penicillopepsin. Towards a Catalytic Mechanism for Acid Proteases
Authors: James, M.N.G. / Hsu, I-N. / Hofmann, T. / Sielecki, A.R.
#6: Journal: Can.J.Biochem. / Year: 1980
Title: An X-Ray Crystallographic Approach to Enzyme Structure and Function
Authors: James, M.N.G.
#7: Journal: Nature / Year: 1978
Title: Structural Evidence for Gene Duplication in the Evolution of the Acid Proteases
Authors: Tang, J. / James, M.N.G. / Hsu, I.N. / Jenkins, J.A. / Blundell, T.L.
#8: Journal: Nature / Year: 1977
Title: Mechanism of Acid Protease Catalysis Based on the Crystal Structure of Penicillopepsin
Authors: James, M.N.G. / Hsu, I.-N. / Delbaere, L.T.J.
#9: Journal: Nature / Year: 1977
Title: Penicillopepsin from Penicillium Janthinellum Crystal Structure at 2.8 Angstroms and Sequence Homology with Porcine Pepsin
Authors: Hsu, I.-N. / Delbaere, L.T.J. / James, M.N.G. / Hofmann, T.
#10: Journal: Adv.Exp.Med.Biol. / Year: 1977
Title: Penicillopepsin. 2.8 Angstroms Structure, Active Site Conformation and Mechanistic Implications
Authors: Hsu, I-N. / Delbaere, L.T.J. / James, M.N.G. / Hofmann, T.
#11: Journal: Biochem.Biophys.Res.Commun. / Year: 1976
Title: The Crystal Structure of Penicillopepsin at 6 Angstroms Resolution
Authors: Hsu, I-N. / Hofmann, T. / Nyburg, S.C. / James, M.N.G.
History
DepositionJun 1, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Jul 17, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_status / software / struct_conn
Item: _pdbx_database_status.process_site / _software.classification / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Jul 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: PENICILLOPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5015
Polymers33,4691
Non-polymers1,0324
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.400, 46.590, 66.290
Angle α, β, γ (deg.)90.00, 115.70, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: RESIDUES 134 AND 315 ARE CIS PROLINES.
Components on special symmetry positions
IDModelComponents
11E-374-

HOH

-
Components

-
Protein , 1 types, 1 molecules E

#1: Protein PENICILLOPEPSIN /


Mass: 33468.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium janthinellum (fungus) / References: UniProt: P00798, penicillopepsin

-
Sugars , 2 types, 2 molecules

#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
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
#4: Sugar ChemComp-ARA / alpha-L-arabinopyranose / Arabinose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
LArapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-arabinopyranoseCOMMON NAMEGMML 1.0
a-L-ArapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 308 molecules

#2: Chemical ChemComp-0P1 / N-[(benzyloxy)carbonyl]-L-alanyl-N-{(1S)-1-[(R)-[(1R)-1-benzyl-2-methoxy-2-oxoethoxy](hydroxy)phosphoryl]-3-methylbutyl }-L-alaninamide / Cbz-Ala-Ala-Leu(P)-(O)-Phe-OMe


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 605.616 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H40N3O9P / References: Cbz-Ala-Ala-Leu(P)-(O)-Phe-OMe
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsXYS IS POORLY DEFINED IN THE ELECTRON DENSITY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.19 %
Crystal grow
*PLUS
Temperature: 18-22 ℃ / pH: 4.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlcomplex1drop
234-40 %satammonium sulfate1drop
30.1 M1dropNaC2H3O2

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 60 Å / Num. all: 29687 / Num. obs: 26564 / Num. measured all: 100309 / Rmerge(I) obs: 0.055

-
Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.15 / Rfactor obs: 0.15 / Highest resolution: 1.7 Å
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 67 306 2739
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 8 Å / Num. reflection obs: 25614 / Rfactor obs: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d0.043
X-RAY DIFFRACTIONx_planar_d0.045
X-RAY DIFFRACTIONx_plane_restr0.019
X-RAY DIFFRACTIONx_chiral_restr0.163

+
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