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- PDB-2r9c: Calpain 1 proteolytic core inactivated by ZLAK-3001, an alpha-ket... -

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Basic information

Entry
Database: PDB / ID: 2r9c
TitleCalpain 1 proteolytic core inactivated by ZLAK-3001, an alpha-ketoamide
ComponentsCalpain-1 catalytic subunit
KeywordsHYDROLASE / PROTEASE / PEPTIDASE / INHIBITOR / ALPHA-KETOAMIDE / Membrane / Thiol protease
Function / homology
Function and homology information


calpain-1 / Degradation of the extracellular matrix / positive regulation of leukocyte tethering or rolling / mammary gland involution / calcium-dependent cysteine-type endopeptidase activity / receptor catabolic process / negative regulation of actin filament polymerization / self proteolysis / cornified envelope / regulation of catalytic activity ...calpain-1 / Degradation of the extracellular matrix / positive regulation of leukocyte tethering or rolling / mammary gland involution / calcium-dependent cysteine-type endopeptidase activity / receptor catabolic process / negative regulation of actin filament polymerization / self proteolysis / cornified envelope / regulation of catalytic activity / positive regulation of vascular permeability / response to arsenic-containing substance / response to angiotensin / negative regulation of non-canonical NF-kappaB signal transduction / Neutrophil degranulation / positive regulation of cardiac muscle cell apoptotic process / protein autoprocessing / cytoskeletal protein binding / protein catabolic process / cellular response to hydrogen peroxide / peptidase activity / lysosome / calcium ion binding / enzyme binding / mitochondrion / proteolysis / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Calpain subdomain III / Peptidase C2, calpain, domain III / calpain_III / Peptidase C2, calpain, large subunit, domain III / Peptidase C2, calpain family / Calpain large subunit, domain III superfamily / Calpain large subunit, domain III / Peptidase C2, calpain, catalytic domain / Calpain family cysteine protease / Cysteine proteinase, calpain-type, catalytic domain profile. ...Calpain subdomain III / Peptidase C2, calpain, domain III / calpain_III / Peptidase C2, calpain, large subunit, domain III / Peptidase C2, calpain family / Calpain large subunit, domain III superfamily / Calpain large subunit, domain III / Peptidase C2, calpain, catalytic domain / Calpain family cysteine protease / Cysteine proteinase, calpain-type, catalytic domain profile. / Calpain-like thiol protease family. / EF-hand domain pair / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-GRD / Calpain-1 catalytic subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsQian, J. / Campbell, R.L. / Davies, P.L.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Cocrystal structures of primed side-extending alpha-ketoamide inhibitors reveal novel calpain-inhibitor aromatic interactions.
Authors: Qian, J. / Cuerrier, D. / Davies, P.L. / Li, Z. / Powers, J.C. / Campbell, R.L.
History
DepositionSep 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _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: Calpain-1 catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7309
Polymers38,8051
Non-polymers9258
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.430, 70.250, 110.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Calpain-1 catalytic subunit / / Calpain-1 large subunit / Calcium-activated neutral proteinase 1 / CANP 1 / Calpain mu-type / ...Calpain-1 large subunit / Calcium-activated neutral proteinase 1 / CANP 1 / Calpain mu-type / muCANP / Micromolar-calpain


Mass: 38804.551 Da / Num. of mol.: 1 / Fragment: residues: 27-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Capn1, Cls1 / Plasmid: PET24D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P97571, calpain-1

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Non-polymers , 5 types, 313 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GRD / benzyl (S)-1-((2S,3S)-1-(3-(6-amino-9H-purin-9-yl)propylamino)-2-hydroxy-1-oxopentan-3-ylamino)-4-methyl-1-oxopentan-2-ylcarbamate


Mass: 554.641 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H38N8O5
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.02 Å3/Da / Density % sol: 39.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.5 M NaCl, 10 mM CaCl2, and 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 24, 2007 / Details: mirrors
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→59.235 Å / Num. all: 29716 / Num. obs: 29944 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 15.1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1kxr chain a

1kxr


Resolution: 1.8→27.6 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.106 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1957 1505 5.1 %RANDOM
Rwork0.15613 ---
obs0.15818 28210 99.24 %-
all-28210 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.281 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2594 0 57 305 2956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222771
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9583764
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4975335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76724.532139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80615462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5571515
X-RAY DIFFRACTIONr_chiral_restr0.1160.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022140
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21376
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21888
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0810.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0721.51662
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.74522615
X-RAY DIFFRACTIONr_scbond_it2.4631306
X-RAY DIFFRACTIONr_scangle_it3.9024.51142
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 113 -
Rwork0.169 2045 -
obs--98.36 %

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