[English] 日本語
Yorodumi
- PDB-1nx3: Calpain Domain VI in Complex with the Inhibitor PD150606 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nx3
TitleCalpain Domain VI in Complex with the Inhibitor PD150606
ComponentsCalcium-dependent protease, small subunit
KeywordsHYDROLASE / CALCIUM BINDING
Function / homology
Function and homology information


Degradation of the extracellular matrix / calpain complex / calcium-dependent cysteine-type endopeptidase activity / calcium ion binding / proteolysis / plasma membrane / cytoplasm
Similarity search - Function
EF-hand / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
3-(4-IODO-PHENYL)-2-MERCAPTO-PROPIONIC ACID / Calpain small subunit 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsTodd, B. / Moore, D. / Deivanayagam, C.C.S. / Lin, G.-D. / Chattopadhyay, D. / Maki, M. / Wang, K.K.W. / Narayana, S.V.L.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: A structural model for the inhibition of calpain by calpastatin: crystal structures of the native domain VI of calpain and its complexes with calpastatin peptide and a small molecule inhibitor.
Authors: Todd, B. / Moore, D. / Deivanayagam, C.C.S. / Lin, G.-D. / Chattopadhyay, D. / Maki, M. / Wang, K.K.W. / Narayana, S.V.L.
History
DepositionFeb 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 2, 2012Group: Structure summary
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_label_seq_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: Calcium-dependent protease, small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3526
Polymers19,8831
Non-polymers4685
Water1,00956
1
A: Calcium-dependent protease, small subunit
hetero molecules

A: Calcium-dependent protease, small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,70412
Polymers39,7672
Non-polymers93710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area5820 Å2
ΔGint-101 kcal/mol
Surface area16230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.578, 78.578, 77.891
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Calcium-dependent protease, small subunit / Calpain regulatory subunit / Calcium-activated neutral proteinase / CANP


Mass: 19883.477 Da / Num. of mol.: 1 / Fragment: Domain VI
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CAPNS1 OR CAPN4 / Production host: Escherichia coli (E. coli) / References: UniProt: P04574
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ISA / 3-(4-IODO-PHENYL)-2-MERCAPTO-PROPIONIC ACID / PD150606


Mass: 308.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9IO2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 4.22 Å3/Da / Density % sol: 64.76 %
Crystal growMethod: vapor diffusion, hanging drop
Details: PEG 6000, BME, EDTA, CaCl2, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 6.7 / PH range high: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMsodium cacodylate1reservoirpH5.5-6.7
223 %(w/v)PEG60001reservoir
35 mMbeta-mercaptoethanol1reservoir
42 mMEDTA1reservoir
52 mM1reservoirCaCl2
615 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionLowest resolution: 100 Å / Num. all: 10626 / Num. obs: 10626 / % possible obs: 99.9 % / Observed criterion σ(F): 2.45 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.8
Reflection
*PLUS
Highest resolution: 2.45 Å

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→100 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1063 10 %random
Rwork0.21 ---
obs0.21 10626 --
all-10626 --
Refinement stepCycle: LAST / Resolution: 2.45→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 17 56 1468
Refinement
*PLUS
Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.0066
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.094

+
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