[English] 日本語
Yorodumi
- PDB-8b5f: Human cathepsin B in complex with the carbamate inhibitor 31 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b5f
TitleHuman cathepsin B in complex with the carbamate inhibitor 31
ComponentsCathepsin B
KeywordsHYDROLASE / Cathepsin B / Cysteine cathepsin / Inhibitor / Carbamate / Peptidomimetic Cysteine proteinases
Function / homology
Function and homology information


cathepsin B / peptidase inhibitor complex / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / decidualization ...cathepsin B / peptidase inhibitor complex / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / decidualization / collagen catabolic process / epithelial cell differentiation / cysteine-type peptidase activity / collagen binding / MHC class II antigen presentation / proteolysis involved in protein catabolic process / melanosome / peptidase activity / collagen-containing extracellular matrix / regulation of apoptotic process / ficolin-1-rich granule lumen / lysosome / symbiont entry into host cell / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / Neutrophil degranulation / perinuclear region of cytoplasm / proteolysis / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Peptidase C1A, propeptide / Peptidase family C1 propeptide / 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 ...Peptidase C1A, propeptide / Peptidase family C1 propeptide / 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. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Chem-P9U / Cathepsin B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsRubesova, P. / Guetschow, M. / Mares, M.
Funding support Czech Republic, European Union, 2items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech Republic Czech Republic
European Regional Development FundEuropean Union
CitationJournal: To Be Published
Title: Human cathepsin B in complex with the carbamate inhibitor 31
Authors: Rubesova, P. / Guetschow, M. / Mares, M.
History
DepositionSep 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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: Cathepsin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7283
Polymers27,9561
Non-polymers7722
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint2 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.573, 81.565, 93.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cathepsin B / APP secretase / APPS / Cathepsin B1


Mass: 27956.156 Da / Num. of mol.: 1 / Mutation: S115A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSB, CPSB / Plasmid: pPICZ(alpha) A / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P07858, cathepsin B
#2: Chemical ChemComp-P9U / (2S)-2-[[(2S)-2-[[3-chloranyl-4-[[3-phenyl-2-(phenylmethyl)propanoyl]amino]phenoxy]carbonylamino]-3-cyclohexyl-propanoyl]amino]-3-phenyl-propanoic acid / (2~{S})-2-[[(2~{S})-2-[[3-chloranyl-4-[[3-phenyl-2-(phenylmethyl)propanoyl]amino]phenoxy]carbonylamino]-3-cyclohexyl-propanoyl]amino]-3-phenyl-propanoic acid


Mass: 710.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H44ClN3O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Sodium Acetate pH 5.5, 30% PEG 5000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.7→46.76 Å / Num. obs: 26540 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 28.907 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.247 / Rrim(I) all: 0.257 / Χ2: 0.717 / Net I/σ(I): 9.34 / Num. measured all: 342373
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.812.8513.160.8353806419841870.333.29199.7
1.8-1.9312.5732.0041.3649989397839760.5462.08999.9
1.93-2.0813.431.0722.7249462368436830.8241.115100
2.08-2.2813.260.6314.745283341934150.9240.65799.9
2.28-2.5512.6960.3817.3140030315331530.9680.397100
2.55-2.9413.5090.23411.8837110275027470.9890.24399.9
2.94-3.612.3160.12520.6729214237723720.9960.1399.8
3.6-5.0713.10.06735.3424824189618950.9990.0799.9
5.07-46.7611.380.05437.0712655111511120.9990.05799.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.342
Highest resolutionLowest resolution
Rotation40.78 Å1.91 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDS1.12data reduction
XSCALE20220220data scaling
MOLREP11.7.02phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8B4T

8b4t


Resolution: 1.7→46.76 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.1778 / WRfactor Rwork: 0.1461 / FOM work R set: 0.7954 / SU B: 3.155 / SU ML: 0.093 / SU R Cruickshank DPI: 0.1117 / SU Rfree: 0.1054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 1328 5 %RANDOM
Rwork0.1747 ---
obs0.1762 25215 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.77 Å2 / Biso mean: 23.241 Å2 / Biso min: 11.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0 Å2
2---0.74 Å2-0 Å2
3---0.97 Å2
Refinement stepCycle: final / Resolution: 1.7→46.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 29 186 2175
Biso mean--32.82 32.39 -
Num. residues----255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132114
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181799
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.6572880
X-RAY DIFFRACTIONr_angle_other_deg1.4661.5944208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0385266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.87222.804107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44515313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0031510
X-RAY DIFFRACTIONr_chiral_restr0.0830.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022456
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02463
LS refinement shellResolution: 1.7→1.74 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.321 94 -
Rwork0.352 1769 -
obs--99.52 %

+
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