[English] 日本語
Yorodumi
- PDB-1sp4: Crystal structure of NS-134 in complex with bovine cathepsin B: a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sp4
TitleCrystal structure of NS-134 in complex with bovine cathepsin B: a two headed epoxysuccinyl inhibitor extends along the whole active site cleft
Components(Cathepsin B) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / cathepsin B / epoxysuccinyl-based inhibitors / inhibitor design / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Trafficking and processing of endosomal TLR / Collagen degradation / cathepsin B / MHC class II antigen presentation / regulation of catalytic activity / Neutrophil degranulation / proteolysis involved in protein catabolic process / melanosome / endopeptidase activity / lysosome ...Trafficking and processing of endosomal TLR / Collagen degradation / cathepsin B / MHC class II antigen presentation / regulation of catalytic activity / Neutrophil degranulation / proteolysis involved in protein catabolic process / melanosome / endopeptidase activity / lysosome / apical plasma membrane / cysteine-type endopeptidase activity / extracellular space
Similarity search - Function
Peptidase C1A, propeptide / Peptidase family C1 propeptide / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 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 ...Peptidase C1A, propeptide / Peptidase family C1 propeptide / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / 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 peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cysteine proteinases / Cathepsin B; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NS-134 TWO HEADED EPOXYSUCCINYL INHIBITOR / Chem-EP2 / Cathepsin B
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsStern, I. / Schaschke, N. / Moroder, L. / Turk, D.
CitationJournal: Biochem.J. / Year: 2004
Title: Crystal structure of NS-134 in complex with bovine cathepsin B: a two-headed epoxysuccinyl inhibitor extends along the entire active-site cleft.
Authors: Stern, I. / Schaschke, N. / Moroder, L. / Turk, D.
History
DepositionMar 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 1.4Feb 12, 2014Group: Refinement description
Revision 1.5Oct 11, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _software.classification / _software.name
Revision 1.6Mar 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 999SEQUENCE THE PROTEIN IS POSTRANSLATIONALLY MODIFIED. AFTER THE ENZYME IS PROCESSED, THE PEPTIDE ...SEQUENCE THE PROTEIN IS POSTRANSLATIONALLY MODIFIED. AFTER THE ENZYME IS PROCESSED, THE PEPTIDE BOND BETWEEN THE RESIDUES 48 49 IS CLEAVED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cathepsin B
B: Cathepsin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1183
Polymers27,5352
Non-polymers5841
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-34 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.064, 73.064, 141.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein/peptide Cathepsin B


Mass: 5300.875 Da / Num. of mol.: 1 / Fragment: light chain / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: kidney / References: UniProt: P07688, cathepsin B
#2: Protein Cathepsin B


Mass: 22233.732 Da / Num. of mol.: 1 / Fragment: heavy chain / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: kidney / References: UniProt: P07688, cathepsin B
#3: Chemical ChemComp-EP2 / methyl N-[(2S)-4-{[(1S)-1-{[(2S)-2-carboxypyrrolidin-1-yl]carbonyl}-3-methylbutyl]amino}-2-hydroxy-4-oxobutanoyl]-L-leucylglycylglycinate / NS-134


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 583.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H41N5O10
Details: LEU-GLY-MEU. EPO is linked to the LEU-GLY-MEU as well as LEU-PRO. The inhibitor was chemically synthesized.
References: NS-134 TWO HEADED EPOXYSUCCINYL INHIBITOR
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE INHIBITOR IS A TWO HEADED EPOXYSUCCINYL INHIBITOR. THE EPOXY GROUP OPENS UPON REACTION WITH THE ...THE INHIBITOR IS A TWO HEADED EPOXYSUCCINYL INHIBITOR. THE EPOXY GROUP OPENS UPON REACTION WITH THE ENZYME. THE INHIBITOR HAS TWO C-TERMINI AND NO N TERMINUS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.89 %
Crystal growpH: 3.5 / Details: pH 3.5

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1998 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 20320 / % possible obs: 96 %
Reflection shellResolution: 2.2→2.28 Å / % possible all: 77

-
Processing

Software
NameClassification
MAINrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→10 Å /
RfactorNum. reflection
Rwork0.194 -
all-19372
obs-19372
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å20 Å2
2--1 Å20 Å2
3---1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 0 41 176 2143
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.0135
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.635
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it

+
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