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- PDB-1nx3: Calpain Domain VI in Complex with the Inhibitor PD150606 -

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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


High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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