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- PDB-2nqi: Calpain 1 proteolytic core inactivated by WR13(R,R), an epoxysucc... -

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Basic information

Entry
Database: PDB / ID: 2nqi
TitleCalpain 1 proteolytic core inactivated by WR13(R,R), an epoxysuccinyl-type inhibitor.
ComponentsCalpain-1 catalytic subunit
KeywordsHYDROLASE / epoxide / epoxysuccinyl / protease / peptidase / proteinase / inactivator / inhibitor
Function / homology
Function and homology information


calpain-1 / Degradation of the extracellular matrix / protein catabolic process at postsynapse / mammary gland involution / positive regulation of leukocyte tethering or rolling / calcium-dependent cysteine-type endopeptidase activity / regulation of catalytic activity / negative regulation of actin filament polymerization / receptor catabolic process / cornified envelope ...calpain-1 / Degradation of the extracellular matrix / protein catabolic process at postsynapse / mammary gland involution / positive regulation of leukocyte tethering or rolling / calcium-dependent cysteine-type endopeptidase activity / regulation of catalytic activity / negative regulation of actin filament polymerization / receptor catabolic process / cornified envelope / self proteolysis / 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 / presynapse / peptidase activity / postsynapse / postsynaptic density / lysosome / glutamatergic synapse / 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 ...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-NQI / Calpain-1 catalytic subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsCuerrier, D. / Davies, P.L. / Campbell, R.L. / Moldoveanu, T.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Development of Calpain-specific Inactivators by Screening of Positional Scanning Epoxide Libraries
Authors: Cuerrier, D. / Moldoveanu, T. / Campbell, R.L. / Kelly, J. / Yoruk, B. / Verhelst, S.H.L. / Greenbaum, D. / Bogyo, M. / Davies, P.L.
History
DepositionOct 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 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 / pdbx_struct_conn_angle / 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 / _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.pdbx_leaving_atom_flag / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)39,4854
Polymers38,8051
Non-polymers6813
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.369, 70.060, 110.743
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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: Calpain catalytic domain, residues 27-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Capn1, Cls1 / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P97571, calpain-1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NQI / N~2~-[(2S)-2-{[(2R)-4-ETHOXY-2-HYDROXY-4-OXOBUTANOYL]AMINO}PENT-4-ENOYL]-L-ARGINYL-L-TRYPTOPHANAMIDE


Mass: 600.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H40N8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 39.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Expansion around 1.1-1.7 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 2006 / Details: OSMIC CONFOCAL MIRROR
RadiationMonochromator: OSMIC CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.04→59.3 Å / Num. obs: 19556 / % possible obs: 99.3 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 11
Reflection shellResolution: 2.04→2.12 Å / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2235 / % possible all: 72.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G8J

2g8j


Resolution: 2.04→59.23 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.885 / SU B: 4.443 / SU ML: 0.127 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24735 1057 5.1 %RANDOM
Rwork0.18066 ---
obs0.1841 15556 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.674 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.04→59.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2634 0 45 153 2832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222746
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.9523725
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6895321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55324.348138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98815459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4811516
X-RAY DIFFRACTIONr_chiral_restr0.1210.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022113
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.21352
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21858
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2174
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0810.29
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2810.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0881.51661
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76222603
X-RAY DIFFRACTIONr_scbond_it2.5331286
X-RAY DIFFRACTIONr_scangle_it3.6844.51122
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.04→2.091 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 81 -
Rwork0.189 1300 -
obs--92.81 %

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