[English] 日本語
Yorodumi
- PDB-1khp: Monoclinic form of papain/ZLFG-DAM covalent complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1khp
TitleMonoclinic form of papain/ZLFG-DAM covalent complex
Components
  • Papain
  • peptidic inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEASE INHIBITOR / DIAZOMETHYLKETONE INHIBITOR / IRREVERSIBLE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


papain / serpin family protein binding / cysteine-type peptidase activity / proteolysis
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
L-leucyl-N-(2-oxopropyl)-L-phenylalaninamide / Papain
Similarity search - Component
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJanowski, R. / Kozak, M. / Jankowska, E. / Grzonka, Z. / Jaskolski, M.
Citation
Journal: J.Pept.Res. / Year: 2004
Title: Two polymorphs of a covalent complex between papain and a diazomethylketone inhibitor
Authors: Janowski, R. / Kozak, M. / Jankowska, E. / Grzonka, Z. / Jaskolski, M.
#1: Journal: ACTA BIOCHIM.POL. / Year: 1997
Title: Crystallization and preliminary crystallographic studies of a new crystal form of papain from Carica papaya.
Authors: Kozak, M. / Kozian, E. / Grzonka, Z. / Jaskolski, M.
#2: Journal: ACTA BIOCHIM.POL. / Year: 2001
Title: Structural studies of cysteine proteases and their inhibitors
Authors: Grzonka, Z. / Jankowska, E. / Wieczerzak, E. / Kasprzykowski, F. / Lankiewicz, L. / Wiczk, W. / Drabik, P. / Ciarkowski, J. / Janowski, R. / Kozak, M. / Jaskolski, M. / Grubb, A.
#3: Journal: Biochemistry / Year: 1976
Title: Binding of chloromethyl ketone substrate analogues to crystalline papain.
Authors: Drenth, J. / Kalk, K.H. / Swen, H.M.
#4: Journal: ACTA CRYSTALLOGR.,SECT.B / Year: 1992
Title: Structure of monoclinic papain at 1.60 Angstroms resolution.
Authors: Pickersgill, R.W. / Harris, G.W. / Garman, E.
#5: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 1999
Title: Binding modes of a new epoxysuccinyl-peptide inhibitor of cysteine proteases. Where and how do cysteine proteases express their selectivity?
Authors: Czaplewski, C. / Grzonka, Z. / Jaskolski, M. / Kasprzykowski, F. / Kozak, M. / Politowska, E. / Ciarkowski, J.
History
DepositionNov 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Papain
I: peptidic inhibitor


Theoretical massNumber of molelcules
Total (without water)23,9642
Polymers23,9642
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-6 kcal/mol
Surface area9530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.44, 48.93, 52.69
Angle α, β, γ (deg.)90.00, 112.42, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Papain / Papaya proteinase I / PPI


Mass: 23452.301 Da / Num. of mol.: 1 / Fragment: Papain, Residues 134-345 / Source method: isolated from a natural source / Source: (natural) Carica papaya (papaya) / References: UniProt: P00784, papain
#2: Protein/peptide peptidic inhibitor


Type: Peptide-like / Class: Inhibitor / Mass: 512.001 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: L-leucyl-N-(2-oxopropyl)-L-phenylalaninamide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PEPTIDIC INHIBITOR IS COVALENTLY LINKED TO THE SG ATOM OF CYS 25 OF THE PROTEIN VIA A ...THE PEPTIDIC INHIBITOR IS COVALENTLY LINKED TO THE SG ATOM OF CYS 25 OF THE PROTEIN VIA A METHYLKETONE GROUP. THE NON-STANDARD TRIPEPTIDE IS N-TERMINALLY PROTECTED BY THE BENZYLOXYCARBONYL-GROUP PHQ WHICH IS NOT VISIBLE IN ELECTRON DENSITY
Has protein modificationY
Nonpolymer detailsTHE PEPTIDIC INHIBITOR IS COVALENTLY LINKED TO THE SG ATOM OF CYS 25 OF THE PROTEIN VIA A ...THE PEPTIDIC INHIBITOR IS COVALENTLY LINKED TO THE SG ATOM OF CYS 25 OF THE PROTEIN VIA A METHYLKETONE GROUP. THE NON-STANDARD TRIPEPTIDE IS N-TERMINALLY PROTECTED BY THE BENZYLOXYCARBONYL-GROUP PHQ WHICH IS NOT VISIBLE IN ELECTRON DENSITY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9.2
Details: 68% methanol/ethanol (2:1), 34 mM NaCl, 50 mM 2-aminoethanol/HCl, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 292 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
134 mM1reservoirNaCl
250 mM2-aminoethanol-HCl1reservoirpH9.2
330 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 9, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 12041 / Num. obs: 12041 / % possible obs: 88.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 6.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.74 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2 / % possible all: 75.1
Reflection
*PLUS
Num. measured all: 57694
Reflection shell
*PLUS
% possible obs: 75.1 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PPN

1ppn


Resolution: 2→10 Å / SU B: 6.19632 / SU ML: 0.16795 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.2612 / ESU R Free: 0.19839 / Stereochemistry target values: Engh & Huber
Details: MAXIMUM LIKELIHOOD ALGORITHM. TLS PARAMETERS WERE USED. THE PHQ (CARBOBENZOXY- OR BENZYLOXYCARBONYL-) BLOCKING GROUP AT THE N-TERMINUS OF THE INHIBITOR IS NOT VISIBLE IN ELECTRON DENSITY DUE ...Details: MAXIMUM LIKELIHOOD ALGORITHM. TLS PARAMETERS WERE USED. THE PHQ (CARBOBENZOXY- OR BENZYLOXYCARBONYL-) BLOCKING GROUP AT THE N-TERMINUS OF THE INHIBITOR IS NOT VISIBLE IN ELECTRON DENSITY DUE TO DISORDER AND WAS NOT INCLUDED IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1165 9.8 %RANDOM
Rwork0.18 ---
all0.185 10783 --
obs0.185 10783 88.8 %-
Displacement parametersBiso mean: 22.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å20.12 Å2
2--0.57 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 0 53 1732
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.021
X-RAY DIFFRACTIONp_angle_d0.0250.03
X-RAY DIFFRACTIONp_angle_deg1.663
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.7931.5
X-RAY DIFFRACTIONp_mcangle_it1.32
X-RAY DIFFRACTIONp_scbond_it2.4513
X-RAY DIFFRACTIONp_scangle_it3.7844.5
X-RAY DIFFRACTIONp_plane_restr0.0070.02
X-RAY DIFFRACTIONp_chiral_restr0.1080.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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