[English] 日本語
Yorodumi
- PDB-1csb: Crystal structure of cathepsin b inhibited with CA030 at 2.1 angs... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1csb
TitleCrystal structure of cathepsin b inhibited with CA030 at 2.1 angstroms resolution: A basis for the design of specific epoxysuccinyl inhibitors
Components
  • CATHEPSIN B heavy chain
  • CATHEPSIN B light chain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PAPAIN-LIKE LYSOSOMAL DICARBOXY-PEPTIDASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


cathepsin B / peptidase inhibitor complex / endolysosome lumen / thyroid hormone generation / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / decidualization / Collagen degradation ...cathepsin B / peptidase inhibitor complex / endolysosome lumen / thyroid hormone generation / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / decidualization / Collagen degradation / collagen catabolic process / collagen binding / epithelial cell differentiation / MHC class II antigen presentation / cysteine-type peptidase activity / proteolysis involved in protein catabolic process / melanosome / peptidase activity / : / regulation of apoptotic process / ficolin-1-rich granule lumen / lysosome / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / Neutrophil degranulation / symbiont entry into host cell / perinuclear region of cytoplasm / proteolysis / extracellular space / extracellular exosome / extracellular region
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 proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / 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
CA030, ethyl ester of epoxysuccinyl-Ile-Pro-OH / Chem-EP0 / Cathepsin B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsTurk, D. / Bode, W.
Citation
Journal: Biochemistry / Year: 1995
Title: Crystal structure of cathepsin B inhibited with CA030 at 2.0-A resolution: A basis for the design of specific epoxysuccinyl inhibitors.
Authors: Turk, D. / Podobnik, M. / Popovic, T. / Katunuma, N. / Bode, W. / Huber, R. / Turk, V.
#1: Journal: Embo J. / Year: 1991
Title: The Refined 2.15 Angstrom X-Ray Crystal Structure of Human Liver Cathepsin B: The Structural Basis for its Specificity
Authors: Musil, D. / Zucic, D. / Turk, D. / Engh, R.A. / Mayr, I. / Huber, R. / Popovic, T. / Turk, V. / Towatari, T. / Katunuma, N. / Bode, W.
History
DepositionDec 9, 1994Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 1.3Aug 31, 2011Group: Non-polymer description
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.details / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CATHEPSIN B light chain
B: CATHEPSIN B heavy chain
D: CATHEPSIN B light chain
E: CATHEPSIN B heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0486
Polymers55,3044
Non-polymers7452
Water9,764542
1
A: CATHEPSIN B light chain
B: CATHEPSIN B heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0243
Polymers27,6522
Non-polymers3721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-26 kcal/mol
Surface area10630 Å2
MethodPISA
2
D: CATHEPSIN B light chain
E: CATHEPSIN B heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0243
Polymers27,6522
Non-polymers3721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-25 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.510, 34.150, 85.530
Angle α, β, γ (deg.)90.00, 103.10, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO B 138 / 2: CIS PROLINE - PRO E 138
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.018575, -0.006577, -0.999806), (0.023824, 0.999697, -0.006133), (0.999544, -0.0237, 0.018726)
Vector: 83.332, -25.121, 19.004)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 D 1 .. D 47 A 1 .. A 47 0.432 M1 E 50 .. E 254 B 50 .. B 254 0.562 M1 F 3 .. F 4 C 3 .. C 4 0.456

-
Components

#1: Protein/peptide CATHEPSIN B light chain


Mass: 5213.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: LIVER / Organelle: LYSOSOME / References: UniProt: P07858, cathepsin B
#2: Antibody CATHEPSIN B heavy chain


Mass: 22437.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: LIVER / Organelle: LYSOSOME / References: UniProt: P07858, cathepsin B
#3: Chemical ChemComp-EP0 / N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-isoleucyl-L-proline / epoxy succinyl inhibitor


Type: Peptide-like / Class: Inhibitor / Mass: 372.413 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H28N2O7 / References: CA030, ethyl ester of epoxysuccinyl-Ile-Pro-OH
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.5 Mammonium sulfate1reservoir
20.1 Msodium acetate1reservoir
35 mg/mlprotein1drop

-
Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 51421 / % possible obs: 79.1 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.098
Reflection
*PLUS
Highest resolution: 2 Å / Rmerge(I) obs: 0.098
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.05 Å / % possible obs: 64 %

-
Processing

Software
NameClassification
XDSdata scaling
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementResolution: 2→8 Å / σ(F): 2
Details: THE MINIMAL ATOMIC TEMPERATURE FACTOR WAS SET TO 5.
RfactorNum. reflection
Rwork0.194 -
obs0.194 24924
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3876 0 52 542 4470
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.58
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
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.011

+
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