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- PDB-6cl0: Human caspase-3 in complex with Ac-ATS009-KE -

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Basic information

Entry
Database: PDB / ID: 6cl0
TitleHuman caspase-3 in complex with Ac-ATS009-KE
Components
  • ACE-1MH-ASP-PF5-PHE-1U8
  • Caspase-3 subunit p12
  • Caspase-3 subunit p17
KeywordsHYDROLASE/HYDROLASE Inhibitor / caspase-3 / inhibitor / APOPTOSIS / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex
Function / homology
Function and homology information


caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis ...caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis / response to cobalt ion / cellular response to staurosporine / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / response to anesthetic / Apoptosis induced DNA fragmentation / Apoptotic cleavage of cell adhesion proteins / Caspase activation via Dependence Receptors in the absence of ligand / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / death receptor binding / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / axonal fasciculation / regulation of synaptic vesicle cycle / fibroblast apoptotic process / epithelial cell apoptotic process / Other interleukin signaling / platelet formation / negative regulation of cytokine production / positive regulation of amyloid-beta formation / execution phase of apoptosis / negative regulation of B cell proliferation / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / negative regulation of activated T cell proliferation / T cell homeostasis / neurotrophin TRK receptor signaling pathway / B cell homeostasis / negative regulation of cell cycle / response to tumor necrosis factor / cell fate commitment / response to amino acid / response to X-ray / Pyroptosis / regulation of macroautophagy / Caspase-mediated cleavage of cytoskeletal proteins / response to glucose / response to glucocorticoid / response to UV / keratinocyte differentiation / striated muscle cell differentiation / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / protein maturation / enzyme activator activity / erythrocyte differentiation / hippocampus development / response to nicotine / apoptotic signaling pathway / sensory perception of sound / protein catabolic process / regulation of protein stability / protein processing / response to hydrogen peroxide / response to wounding / neuron differentiation / positive regulation of neuron apoptotic process / response to estradiol / peptidase activity / heart development / protease binding / neuron apoptotic process / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / postsynaptic density / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / DNA damage response / protein-containing complex binding / glutamatergic synapse / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Caspase-like / Rossmann fold - #1460 / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain ...Caspase-like / Rossmann fold - #1460 / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(ACE)(1MH)D(PF5)F(1U8) / Caspase-3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSolania, A.T. / Gonzalez-Paez, G.E. / Wolan, D.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R21AI112796 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM118382 United States
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Selective and Rapid Cell-Permeable Inhibitor of Human Caspase-3.
Authors: Solania, A. / Gonzalez-Paez, G.E. / Wolan, D.W.
History
DepositionMar 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Sep 30, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_molecule_features / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_validate_rmsd_angle / struct_conn / struct_keywords / struct_ref_seq / struct_sheet_range
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Revision 2.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-3 subunit p17
B: Caspase-3 subunit p12
C: ACE-1MH-ASP-PF5-PHE-1U8


Theoretical massNumber of molelcules
Total (without water)33,6943
Polymers33,6943
Non-polymers00
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-31 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.103, 84.140, 96.388
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-255-

HOH

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Components

#1: Protein Caspase-3 subunit p17 / CASP-3


Mass: 19759.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Production host: Escherichia coli (E. coli) / References: UniProt: P42574, caspase-3
#2: Protein Caspase-3 subunit p12 / CASP-3


Mass: 12981.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Production host: Escherichia coli (E. coli) / References: UniProt: P42574, caspase-3
#3: Protein/peptide ACE-1MH-ASP-PF5-PHE-1U8


Type: Peptide-like / Class: CASPASE inhibitor / Mass: 952.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: (ACE)(1MH)D(PF5)F(1U8)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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 Å3/Da / Density % sol: 38.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1:1 dilution with 0.10 M sodium citrate, pH 5.0, 13.6 % PEG6000, 0.010 M DTT, 0.02% NaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 40755 / % possible obs: 92.6 % / Redundancy: 7.6 % / Biso Wilson estimate: 14.62 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.031 / Rrim(I) all: 0.076 / Rsym value: 0.083 / Net I/av σ(I): 19.3 / Net I/σ(I): 28.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1309 / CC1/2: 0.851 / Rpim(I) all: 0.314 / Rrim(I) all: 0.838 / Rsym value: 0.774 / % possible all: 60.2

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Processing

Software
NameVersionClassification
PHENIX(dev_2747: ???)refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JJE

4jje


Resolution: 1.5→42.07 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.164 2057 5.05 %
Rwork0.1402 --
obs0.1414 40752 92.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 0 249 2302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172171
X-RAY DIFFRACTIONf_angle_d1.5232927
X-RAY DIFFRACTIONf_dihedral_angle_d3.7571271
X-RAY DIFFRACTIONf_chiral_restr0.129315
X-RAY DIFFRACTIONf_plane_restr0.01376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4998-1.53470.189910.1741721X-RAY DIFFRACTION62
1.5347-1.5730.20471130.15982050X-RAY DIFFRACTION75
1.573-1.61560.1891320.14982535X-RAY DIFFRACTION92
1.6156-1.66310.18721230.14052669X-RAY DIFFRACTION96
1.6631-1.71680.17891550.13922681X-RAY DIFFRACTION97
1.7168-1.77810.17451280.13922679X-RAY DIFFRACTION97
1.7781-1.84930.15671390.13852587X-RAY DIFFRACTION94
1.8493-1.93350.16351440.14032693X-RAY DIFFRACTION97
1.9335-2.03540.17281640.12772688X-RAY DIFFRACTION98
2.0354-2.1630.14861260.13472700X-RAY DIFFRACTION96
2.163-2.330.16381300.12912701X-RAY DIFFRACTION96
2.33-2.56440.16131530.14082732X-RAY DIFFRACTION98
2.5644-2.93540.15211500.1452653X-RAY DIFFRACTION95
2.9354-3.6980.16261430.13962809X-RAY DIFFRACTION99
3.698-42.08650.16221660.14332797X-RAY DIFFRACTION95
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)
17.14643.82772.69065.3946-1.01283.00760.11730.0063-0.11190.20250.1564-0.12470.33920.1952-0.23480.30350.0409-0.0150.21510.02440.160739.57619.982171.2744
20.7086-0.1365-0.00091.2524-0.25270.78630.03620.0046-0.01760.08750.02220.1497-0.0223-0.0667-0.05980.1121-0.00380.02510.11410.00150.119220.04419.228962.8191
30.75140.0311-0.01960.7894-0.06160.70690.00330.0559-0.1170.04460.01580.09070.0606-0.0654-0.01980.1276-0.00180.00480.1205-0.00130.129823.133814.206855.6226
40.5472-0.0979-0.55110.89130.22070.5747-0.00170.35340.1842-0.2625-0.06790.0837-0.1578-0.07590.06840.1720.0064-0.0140.19070.04420.154624.064120.643839.1609
50.9559-0.35210.60440.8955-0.50451.23210.0151-0.02960.02430.10820.0043-0.0097-0.0986-0.0077-0.02560.1166-0.01510.00650.112-0.00550.103336.06523.337460.3616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 171 )
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 197 )
4X-RAY DIFFRACTION4chain 'B' and (resid 198 through 279 )
5X-RAY DIFFRACTION5chain 'C' and (resid 403 through 405 )

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