[English] 日本語
Yorodumi
- PDB-6p4e: Leishmania mexicana CPB in complex with an aza-nitrile inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p4e
TitleLeishmania mexicana CPB in complex with an aza-nitrile inhibitor
ComponentsCysteine proteinase B
KeywordsHYDROLASE/HYDROLASE INHIBITOR / endopeptidase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


proteolysis involved in protein catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lysosome / cysteine-type endopeptidase activity / extracellular space
Similarity search - Function
Domain of unknown function DUF3586 / Protein of unknown function (DUF3586) / 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. ...Domain of unknown function DUF3586 / Protein of unknown function (DUF3586) / 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
ACETATE ION / Chem-GES / Cysteine proteinase B
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsRibeiro, J.F.R. / Li, C. / De Vita, D. / Emsley, J. / Montanari, C.A.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Other governmentCAPES AUXPE 139/2015 Brazil
CitationJournal: To Be Published
Title: High Resolution X-Ray Crystal Structures of LmCPB2.8 Co-Crystalized with Dipeptidyl Aza-nitrile Inhibitor and Structure Activity Relationships
Authors: Ribeiro, J.F.R. / De Vita, D. / Li, C. / Emsley, J. / Montanari, C.A.
History
DepositionMay 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_database_PDB_obs_spr ...database_2 / pdbx_database_PDB_obs_spr / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine proteinase B
B: Cysteine proteinase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,90415
Polymers46,4202
Non-polymers1,48413
Water8,899494
1
A: Cysteine proteinase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9507
Polymers23,2101
Non-polymers7406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cysteine proteinase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9548
Polymers23,2101
Non-polymers7447
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.636, 82.636, 134.846
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11B-306-

TRS

21B-306-

TRS

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Cysteine proteinase B


Mass: 23210.004 Da / Num. of mol.: 2 / Mutation: N61D, D62N, D65S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Gene: LMCPB, LMCPB2.8 / Plasmid: pET21a / Production host: Escherichia coli (E. coli)
Variant (production host): ArcticExpress (DE3) competent cells
References: UniProt: P36400, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

-
Non-polymers , 6 types, 507 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-GES / 3-tert-butyl-N-[(2S)-1-(2-cyano-1,2-dimethylhydrazinyl)-4-methyl-1-oxopentan-2-yl]-1-methyl-1H-pyrazole-5-carboxamide (non-preferred name)


Mass: 362.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H30N6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: Tris 0.1M pH8, MPD 65%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.35→71.56 Å / Num. obs: 112897 / % possible obs: 99 % / Redundancy: 8.7 % / Biso Wilson estimate: 9.2 Å2 / CC1/2: 0.962 / Rmerge(I) obs: 0.239 / Net I/σ(I): 6.4
Reflection shellResolution: 1.35→1.398 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 10475 / CC1/2: 0.45 / % possible all: 90.5

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kku

3kku


Resolution: 1.35→71.56 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.17
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 5630 5 %Random selection
Rwork0.1899 ---
obs0.1911 112632 98.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→71.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3251 0 102 494 3847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083598
X-RAY DIFFRACTIONf_angle_d1.1414935
X-RAY DIFFRACTIONf_dihedral_angle_d19.0981306
X-RAY DIFFRACTIONf_chiral_restr0.078517
X-RAY DIFFRACTIONf_plane_restr0.007637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3498-1.36520.3541530.32713187X-RAY DIFFRACTION89
1.3652-1.38120.30561720.30383385X-RAY DIFFRACTION93
1.3812-1.39810.33481740.29183406X-RAY DIFFRACTION95
1.3981-1.41580.30672100.29753406X-RAY DIFFRACTION96
1.4158-1.43440.3371780.30033566X-RAY DIFFRACTION97
1.4344-1.45410.28141860.27213536X-RAY DIFFRACTION99
1.4541-1.47480.30681870.25663603X-RAY DIFFRACTION100
1.4748-1.49690.27411750.24133599X-RAY DIFFRACTION100
1.4969-1.52030.26091970.2423637X-RAY DIFFRACTION100
1.5203-1.54520.27641860.23913559X-RAY DIFFRACTION100
1.5452-1.57180.25662320.23143592X-RAY DIFFRACTION100
1.5718-1.60040.25711630.22543609X-RAY DIFFRACTION100
1.6004-1.63120.27981810.22263628X-RAY DIFFRACTION100
1.6312-1.66450.24962120.2263568X-RAY DIFFRACTION100
1.6645-1.70070.24881800.22073589X-RAY DIFFRACTION100
1.7007-1.74030.25371820.21613609X-RAY DIFFRACTION100
1.7403-1.78380.2382030.22133562X-RAY DIFFRACTION100
1.7838-1.8320.23281860.2123608X-RAY DIFFRACTION100
1.832-1.88590.22981830.20813628X-RAY DIFFRACTION100
1.8859-1.94680.2241940.20583559X-RAY DIFFRACTION100
1.9468-2.01640.22971730.20133638X-RAY DIFFRACTION100
2.0164-2.09710.21611610.19243576X-RAY DIFFRACTION100
2.0971-2.19260.19431800.1813635X-RAY DIFFRACTION100
2.1926-2.30820.19311720.17463636X-RAY DIFFRACTION100
2.3082-2.45280.211890.16463592X-RAY DIFFRACTION100
2.4528-2.64220.18192060.15453601X-RAY DIFFRACTION100
2.6422-2.90810.1821810.15093610X-RAY DIFFRACTION100
2.9081-3.32890.15711920.13973631X-RAY DIFFRACTION100
3.3289-4.1940.14252220.12293601X-RAY DIFFRACTION100
4.194-71.66540.17812200.15753646X-RAY DIFFRACTION100

+
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