[English] 日本語
Yorodumi
- PDB-2p86: The high resolution crystal structure of rhodesain, the major cat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2p86
TitleThe high resolution crystal structure of rhodesain, the major cathepsin L protease from T. brucei rhodesiense, bound to inhibitor K11002
ComponentsCysteine protease
KeywordsHYDROLASE / cysteine protease / trypanosoma brucei / neglected disease
Function / homology
Function and homology information


cysteine-type endopeptidase activity / proteolysis
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 ...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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-VS1 / Cysteine protease
Similarity search - Component
Biological speciesTrypanosoma brucei rhodesiense (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsBrinen, L.S. / Marion, R.
CitationJournal: To be Published
Title: THE high resolution structure of rhodesain, the major cathepsin L protease from trypanosoma brucei rhodesiense, illustrates the basis for differences in inhibition profiles from other papain ...Title: THE high resolution structure of rhodesain, the major cathepsin L protease from trypanosoma brucei rhodesiense, illustrates the basis for differences in inhibition profiles from other papain family cysteine proteases
Authors: Marion, R. / Hansell, E. / Caffrey, C. / Roush, W.R. / Brinen, L.S.
History
DepositionMar 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 24, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 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 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,15013
Polymers22,9031
Non-polymers1,24612
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.659, 78.628, 80.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cysteine protease /


Mass: 22903.188 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: Ser to Ala mutation at 172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei rhodesiense (eukaryote)
Species: Trypanosoma brucei / Strain: rhodesiense / Gene: rhodesain / Plasmid: pPIC Z / Production host: Pichia pastoris (fungus) / References: UniProt: Q95PM0, cathepsin L
#2: Chemical ChemComp-VS1 / 3-[[N-[MORPHOLIN-N-YL]-CARBONYL]-PHENYLALANINYL-AMINO]-5- PHENYL-PENTANE-1-SULFONYLBENZENE


Mass: 563.708 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H37N3O5S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 298 K / pH: 9
Details: 1.6M Ammonium Sulfate, 0.1 M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2005 / Details: FLAT MIRROR, RH COATED
RadiationMonochromator: SIDE-SCATTERING CUBEROOT I- BEAM BEND SINGLE CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.16→40.36 Å / Num. obs: 68633 / % possible obs: 91.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 27.2
Reflection shellResolution: 1.16→1.22 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 14.9 / % possible all: 80

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P7U, WITHOUT WATERS OR SMALL MOLECULE INHIBITOR

2p7u


Resolution: 1.16→40.36 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.603 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13 3463 5 %RANDOM
Rwork0.11 ---
obs0.111 65123 91.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.799 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.16→40.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 93 402 2135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221775
X-RAY DIFFRACTIONr_bond_other_d0.0020.021154
X-RAY DIFFRACTIONr_angle_refined_deg1.8761.9652413
X-RAY DIFFRACTIONr_angle_other_deg1.5683.012772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6865230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.12326.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37515250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.184152
X-RAY DIFFRACTIONr_chiral_restr0.120.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02317
X-RAY DIFFRACTIONr_nbd_refined0.2230.2396
X-RAY DIFFRACTIONr_nbd_other0.2010.21354
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2879
X-RAY DIFFRACTIONr_nbtor_other0.1020.2837
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2258
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2540.218
X-RAY DIFFRACTIONr_metal_ion_refined0.3180.239
X-RAY DIFFRACTIONr_metal_ion_other0.2260.238
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3390.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6541.51396
X-RAY DIFFRACTIONr_mcbond_other0.8441.5455
X-RAY DIFFRACTIONr_mcangle_it2.39321737
X-RAY DIFFRACTIONr_scbond_it3.4123821
X-RAY DIFFRACTIONr_scangle_it4.3534.5668
X-RAY DIFFRACTIONr_rigid_bond_restr1.65433663
X-RAY DIFFRACTIONr_sphericity_free9.9723403
X-RAY DIFFRACTIONr_sphericity_bonded4.30832887
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.134 187 -
Rwork0.094 3568 -
obs--68.56 %

+
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