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- PDB-2p0r: Structure of Human Calpain 9 in complex with Leupeptin -

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Basic information

Entry
Database: PDB / ID: 2p0r
TitleStructure of Human Calpain 9 in complex with Leupeptin
Components
  • Calpain-9
  • leupeptin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor complex / alpha-beta protein / Hydrolase / calcium-dependent enzyme / Structural Genomics / Structural Genomics Consortium / SGC / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


calcium-dependent cysteine-type endopeptidase activity / digestion / Degradation of the extracellular matrix / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / calcium ion binding / proteolysis / 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, calcium binding motif / 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
LEUPEPTIN / : / Calpain-9
Similarity search - Component
Biological speciesHomo sapiens (human)
Actinomycetes Streptomyces roseus MA 839-A1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDavis, T.L. / Paramanathan, R. / Walker, J.R. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Davis, T.L. / Paramanathan, R. / Walker, J.R. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structures of Human Minicalpains bound to Inhibitors
Authors: Davis, T.L. / Paramanathan, R. / Walker, J.R. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionMar 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
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_conn_type / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _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

Downloads & links

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Assembly

Deposited unit
A: Calpain-9
B: Calpain-9
D: leupeptin
E: leupeptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1159
Polymers75,9154
Non-polymers2005
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-73 kcal/mol
Surface area27610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.165, 97.165, 173.378
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsOne molecule of the asymmetric unit is the biological assembly

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Components

#1: Protein Calpain-9 / / E.C.3.4.22.52 / Digestive tract-specific calpain / nCL-4 / CG36 protein


Mass: 37527.973 Da / Num. of mol.: 2 / Fragment: minicalpain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPN9, NCL4 / Plasmid: pET28-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: O14815, calpain-1
#2: Protein/peptide leupeptin / /


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 429.578 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Actinomycetes Streptomyces roseus MA 839-A1 (bacteria)
References: NOR: NOR00487, LEUPEPTIN
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE LEUPEPTIN IS SUPPOSED TO BE COVALENTLY CONNECTED TO ACTIVE_SITE CYS 97 OF THE ENZYME TO FORM A ...THE LEUPEPTIN IS SUPPOSED TO BE COVALENTLY CONNECTED TO ACTIVE_SITE CYS 97 OF THE ENZYME TO FORM A HEMITHIOACETAL, BUT THE DISTANCES ARE BEYOND 2.3 ANGSTROMS.
Sequence detailsTHERE IS A DISCREPANCY IN THE NORINE AND PDB NUMBERING, AS NORINE COUNTS ACE AND LEU TOGETHER AS ...THERE IS A DISCREPANCY IN THE NORINE AND PDB NUMBERING, AS NORINE COUNTS ACE AND LEU TOGETHER AS ONE RESIDUE. SO THE DBREF WILL REPORT 4 PDB RESIDUES MATCHING NORINE 3 RESIDUE

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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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 14.7% Peg 8000, 10% glycerol, 0.1M Na-Cacodylate, 0.15M Ammonium sulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 10, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 33145 / Num. obs: 33145 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 9.1 % / Biso Wilson estimate: 53.9 Å2 / Rsym value: 0.083 / Net I/σ(I): 8.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.646 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NQA

1nqa


Resolution: 2.5→19.43 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.905 / SU B: 10.536 / SU ML: 0.226 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.501 / ESU R Free: 0.302
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26889 1491 5.1 %RANDOM
Rwork0.21017 ---
obs0.21321 27861 100 %-
all-27861 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.859 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refine analyzeLuzzati coordinate error obs: 0.372 Å / Luzzati d res low obs: 2.5 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5162 0 5 270 5437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225274
X-RAY DIFFRACTIONr_bond_other_d0.0020.023651
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9337131
X-RAY DIFFRACTIONr_angle_other_deg0.90138798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5455636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97623.667270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52315862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5151539
X-RAY DIFFRACTIONr_chiral_restr0.0790.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025933
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021174
X-RAY DIFFRACTIONr_nbd_refined0.2140.21220
X-RAY DIFFRACTIONr_nbd_other0.1930.23809
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22494
X-RAY DIFFRACTIONr_nbtor_other0.0860.22716
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2274
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0760.23
X-RAY DIFFRACTIONr_metal_ion_refined0.1270.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6211.53349
X-RAY DIFFRACTIONr_mcbond_other0.3621.51306
X-RAY DIFFRACTIONr_mcangle_it1.04925086
X-RAY DIFFRACTIONr_scbond_it1.19932325
X-RAY DIFFRACTIONr_scangle_it1.814.52045
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 94 -
Rwork0.351 1980 -
obs--100 %

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