[English] 日本語
Yorodumi
- PDB-6ay2: Structure of CathB with covalently linked Compound 28 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ay2
TitleStructure of CathB with covalently linked Compound 28
ComponentsCathepsin B
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protease / covalent / inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
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 / cysteine-type peptidase activity / epithelial cell differentiation / collagen binding / MHC class II antigen presentation / proteolysis involved in protein catabolic process / melanosome / peptidase activity / regulation of apoptotic process / collagen-containing extracellular matrix / 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 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
Chem-C1G / Cathepsin B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKiefer, J.R. / Steinbacher, S.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Discovery of Peptidomimetic Antibody-Drug Conjugate Linkers with Enhanced Protease Specificity.
Authors: Wei, B. / Gunzner-Toste, J. / Yao, H. / Wang, T. / Wang, J. / Xu, Z. / Chen, J. / Wai, J. / Nonomiya, J. / Tsai, S.P. / Chuh, J. / Kozak, K.R. / Liu, Y. / Yu, S.F. / Lau, J. / Li, G. / ...Authors: Wei, B. / Gunzner-Toste, J. / Yao, H. / Wang, T. / Wang, J. / Xu, Z. / Chen, J. / Wai, J. / Nonomiya, J. / Tsai, S.P. / Chuh, J. / Kozak, K.R. / Liu, Y. / Yu, S.F. / Lau, J. / Li, G. / Phillips, G.D. / Leipold, D. / Kamath, A. / Su, D. / Xu, K. / Eigenbrot, C. / Steinbacher, S. / Ohri, R. / Raab, H. / Staben, L.R. / Zhao, G. / Flygare, J.A. / Pillow, T.H. / Verma, V. / Masterson, L.A. / Howard, P.W. / Safina, B.
History
DepositionSep 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

-
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)56,7354
Polymers55,9442
Non-polymers7912
Water4,270237
1
A: Cathepsin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3682
Polymers27,9721
Non-polymers3961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cathepsin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3682
Polymers27,9721
Non-polymers3961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.317, 127.243, 70.034
Angle α, β, γ (deg.)90.000, 102.900, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 27972.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSB, CPSB / Production host: Escherichia coli (E. coli) / References: UniProt: P07858, cathepsin B
#2: Chemical ChemComp-C1G / N~1~-[(2S)-1-amino-5-(carbamoylamino)pentan-2-yl]-N'~1~-[(1R)-1-(thiophen-3-yl)ethyl]cyclobutane-1,1-dicarboxamide


Mass: 395.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H29N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: as published

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X1A / Wavelength: 0.98764 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98764 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.515
11-H, -K, H+L20.485
ReflectionResolution: 1.6→46.54 Å / Num. obs: 68898 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 2.896 % / Biso Wilson estimate: 23.312 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.05 / Χ2: 0.995 / Net I/σ(I): 18.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.852.8740.1786.07244550.9590.21898.6
1.85-2.042.9070.08811.96113700.9850.10899.1
2.04-2.342.8880.05618.48113660.9920.06898.5
2.34-2.862.9540.03726.9498340.9960.04698
2.86-3.622.8080.02835.3960400.9970.03496.3
3.62-4.653.0350.02247.5630870.9980.02695.8
4.65-6.792.8330.02148.5118490.9980.02594.4
6.79-10.863.0530.02153.76830.9980.02594.3
10.86-46.543.2240.01957.632140.9990.02391.8

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→46.54 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.266 / SU ML: 0.044 / SU R Cruickshank DPI: 0.0164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.016 / ESU R Free: 0.015
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1765 3826 5.6 %RANDOM
Rwork0.1613 ---
obs0.1622 65070 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 52.1 Å2 / Biso mean: 20.342 Å2 / Biso min: 8.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.12 Å20 Å20.59 Å2
2--4.32 Å20 Å2
3----8.44 Å2
Refinement stepCycle: final / Resolution: 1.6→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3911 0 40 237 4188
Biso mean--25.04 19.77 -
Num. residues----509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194062
X-RAY DIFFRACTIONr_bond_other_d0.0010.023542
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.9375538
X-RAY DIFFRACTIONr_angle_other_deg0.73138187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3155507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64923.956182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25815583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2971518
X-RAY DIFFRACTIONr_chiral_restr0.0620.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214711
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02969
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 249 -
Rwork0.216 4833 -
all-5082 -
obs--97.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8054-0.03520.17310.88410.01032.3528-0.015-0.02740.12810.09510.02450.0296-0.4771-0.0248-0.00950.10820.00510.00920.0523-0.00480.02245.8574-0.628132.5479
20.779-0.0239-0.05940.9715-0.01492.1993-0.00530.0447-0.1205-0.12650.02790.02150.45990.0054-0.02260.1120.0002-0.00810.0497-0.00670.019421.4953-24.83966.9334
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 254
2X-RAY DIFFRACTION2B1 - 254

+
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://pdbjlvh1.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