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- PDB-4phk: The Structural Basis of Differential Inhibition of Human Calpain ... -

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Basic information

Entry
Database: PDB / ID: 4phk
TitleThe Structural Basis of Differential Inhibition of Human Calpain by Indole and Phenyl alpha-Mercaptoacrylic Acids. The complex with (Z)-3-(4-chlorophenyl)-2-mercaptoacrylic acid
ComponentsCalpain small subunit 1
KeywordsHYDROLASE / Domain VI / PEF(S) / Calcium Binding / Protease
Function / homology
Function and homology information


calpain complex / calcium-dependent cysteine-type endopeptidase activity / Formation of the cornified envelope / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of macroautophagy / Degradation of the extracellular matrix / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular exosome ...calpain complex / calcium-dependent cysteine-type endopeptidase activity / Formation of the cornified envelope / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of macroautophagy / Degradation of the extracellular matrix / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular exosome / membrane / plasma membrane / cytosol
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
(Z)-3-(4-chlorophenyl)-2-mercaptoacrylic acid / Calpain small subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsRizkallah, P.J. / Allemann, R.K. / Adams, S.E. / Miller, D.J. / Hallett, M.B. / Robinson, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G0701192 United Kingdom
CitationJournal: J.Struct.Biol. / Year: 2014
Title: The structural basis of differential inhibition of human calpain by indole and phenyl alpha-mercaptoacrylic acids.
Authors: Adams, S.E. / Rizkallah, P.J. / Miller, D.J. / Robinson, E.J. / Hallett, M.B. / Allemann, R.K.
History
DepositionMay 6, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Other
Revision 2.0Sep 13, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1May 8, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calpain small subunit 1
B: Calpain small subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,78312
Polymers40,0332
Non-polymers75010
Water2,522140
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-110 kcal/mol
Surface area16140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.540, 80.090, 56.890
Angle α, β, γ (deg.)90.00, 91.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calpain small subunit 1 / CSS1 / Calcium-activated neutral proteinase small subunit / CANP small subunit / Calcium-dependent ...CSS1 / Calcium-activated neutral proteinase small subunit / CANP small subunit / Calcium-dependent protease small subunit / CDPS / Calcium-dependent protease small subunit 1 / Calpain regulatory subunit


Mass: 20016.607 Da / Num. of mol.: 2 / Fragment: residues 96-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAPNS1, CAPN4, CAPNS / Production host: Escherichia coli (E. coli) / References: UniProt: P04632
#2: Chemical ChemComp-2UB / (Z)-3-(4-chlorophenyl)-2-mercaptoacrylic acid


Mass: 214.669 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7ClO2S
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PROTEIN WAS CRYSTALLIZED FROM 12% PEG6000, 20 MM CACL2, 50 MM CACODYLATE BUFFER, PH7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9673 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9673 Å / Relative weight: 1
ReflectionResolution: 2.05→80.09 Å / Num. all: 87320 / Num. obs: 25589 / % possible obs: 91.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.8
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 2.3 / % possible all: 70

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 2.05→80.09 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.885 / SU B: 14.24 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27936 1289 5.1 %RANDOM
Rwork0.23073 ---
obs0.23333 24048 90.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.244 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å2-1.03 Å2
2--1.24 Å20 Å2
3----0.3 Å2
Refinement stepCycle: 1 / Resolution: 2.05→80.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 34 140 2980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192899
X-RAY DIFFRACTIONr_bond_other_d0.0020.022671
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.9453905
X-RAY DIFFRACTIONr_angle_other_deg0.93336124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1435348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95824.194155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.10615514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5751522
X-RAY DIFFRACTIONr_chiral_restr0.1140.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023341
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02729
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9342.5161389
X-RAY DIFFRACTIONr_mcbond_other1.9332.5151388
X-RAY DIFFRACTIONr_mcangle_it2.8953.7611735
X-RAY DIFFRACTIONr_mcangle_other2.8953.7611736
X-RAY DIFFRACTIONr_scbond_it2.4712.8861510
X-RAY DIFFRACTIONr_scbond_other2.472.8871511
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.84.2072170
X-RAY DIFFRACTIONr_long_range_B_refined6.64821.613762
X-RAY DIFFRACTIONr_long_range_B_other6.61321.5343739
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.613 67 -
Rwork0.598 1263 -
obs--65.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.96570.37040.36760.9902-0.18581.19940.1699-0.1921-0.02960.1369-0.07770.16180.1314-0.0695-0.09220.1502-0.03810.01950.0402-0.01240.037513.8092-0.139415.1835
22.1103-0.09520.03030.93620.38730.6811-0.05760.0220.0905-0.12330.11230.0225-0.1320.1014-0.05470.1447-0.0186-0.00070.02220.00820.065928.6779.84570.0649
335.9178-28.1742-19.267826.127717.935712.31360.90721.3140.6013-1.2039-1.55720.9244-0.8381-1.07450.650.21950.0267-0.10480.458-0.04380.579113.0321-11.275922.0782
439.0543-15.553631.45839.7897-10.752326.2207-0.10520.73161.0760.4712-0.9271-0.11070.16410.27711.03230.41-0.06010.1240.1498-0.01770.095139.31585.8764-6.8801
52.32823.7654.80976.18567.475110.98070.0132-0.07940.1361-0.0275-0.18020.2520.10960.05430.1670.09120.01550.010.1132-0.00980.041919.027-3.626316.1339
62.10310.4491.45522.74780.97874.1288-0.02870.1013-0.0826-0.00740.13180.0231-0.03890.062-0.10310.14120.01360.08030.0803-0.01370.111429.84623.504-0.5338
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A96 - 268
2X-RAY DIFFRACTION2B96 - 268
3X-RAY DIFFRACTION3A270
4X-RAY DIFFRACTION4B270
5X-RAY DIFFRACTION5A301 - 304
6X-RAY DIFFRACTION6B301 - 304

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