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- PDB-6ckz: Human caspase-3 in complex with Ac-DW3-KE -

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Basic information

Entry
Database: PDB / ID: 6ckz
TitleHuman caspase-3 in complex with Ac-DW3-KE
Components
  • ACE-1MH-ASP-B3L-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 / phospholipase A2 activator activity / Stimulation of the cell death response by PAK-2p34 / 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 / phospholipase A2 activator activity / Stimulation of the cell death response by PAK-2p34 / 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 / cyclin-dependent protein serine/threonine kinase inhibitor activity / death-inducing signaling complex / Apoptotic cleavage of cell adhesion proteins / Caspase activation via Dependence Receptors in the absence of ligand / Apoptosis induced DNA fragmentation / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / axonal fasciculation / regulation of synaptic vesicle cycle / death receptor binding / fibroblast apoptotic process / epithelial cell apoptotic process / platelet formation / Other interleukin signaling / response to anesthetic / execution phase of apoptosis / negative regulation of cytokine production / positive regulation of amyloid-beta formation / Apoptotic cleavage of cellular proteins / negative regulation of B cell proliferation / neurotrophin TRK receptor signaling pathway / negative regulation of activated T cell proliferation / pyroptotic inflammatory response / negative regulation of cell cycle / response to tumor necrosis factor / T cell homeostasis / B cell homeostasis / Pyroptosis / cell fate commitment / regulation of macroautophagy / Caspase-mediated cleavage of cytoskeletal proteins / response to X-ray / response to amino acid / response to glucose / response to UV / keratinocyte differentiation / Degradation of the extracellular matrix / striated muscle cell differentiation / intrinsic apoptotic signaling pathway / response to glucocorticoid / protein maturation / erythrocyte differentiation / response to nicotine / hippocampus development / apoptotic signaling pathway / enzyme activator activity / protein catabolic process / response to hydrogen peroxide / sensory perception of sound / protein processing / regulation of protein stability / response to wounding / neuron differentiation / response to estradiol / peptidase activity / positive regulation of neuron apoptotic process / 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(B3L)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 / pdbx_molecule_features ...atom_site / 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 / _pdbx_poly_seq_scheme.pdb_seq_num ..._atom_site.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 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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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-B3L-PHE-1U8


Theoretical massNumber of molelcules
Total (without water)33,5843
Polymers33,5843
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: previously determined
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.095, 83.892, 95.863
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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-B3L-PHE-1U8


Type: Peptide-like / Class: CASPASE inhibitor / Mass: 842.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: (ACE)(1MH)D(B3L)F(1U8)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.01 Å3/Da / Density % sol: 38.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 1:1 dilution with 0.10 M sodium citrate, pH 5.4, 15.2 % 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 17, 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: 41773 / % possible obs: 95.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 16.46 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.027 / Rrim(I) all: 0.069 / Rsym value: 0.063 / Net I/av σ(I): 18.2 / Net I/σ(I): 28.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1635 / CC1/2: 0.889 / Rpim(I) all: 0.228 / Rrim(I) all: 0.509 / Rsym value: 0.452 / % possible all: 75.8

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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→41.946 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1714 2101 5.03 %
Rwork0.1531 --
obs0.1541 41762 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→41.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 0 206 2176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072056
X-RAY DIFFRACTIONf_angle_d1.9852771
X-RAY DIFFRACTIONf_dihedral_angle_d4.1841682
X-RAY DIFFRACTIONf_chiral_restr0.063302
X-RAY DIFFRACTIONf_plane_restr0.005354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.5350.25481140.21222074X-RAY DIFFRACTION76
1.535-1.57330.21681310.19482375X-RAY DIFFRACTION88
1.5733-1.61590.2091310.17462662X-RAY DIFFRACTION97
1.6159-1.66340.18971270.1692675X-RAY DIFFRACTION98
1.6634-1.71710.19371520.1632730X-RAY DIFFRACTION99
1.7171-1.77850.16421280.15552673X-RAY DIFFRACTION98
1.7785-1.84970.13771380.14912644X-RAY DIFFRACTION96
1.8497-1.93390.18691430.15692691X-RAY DIFFRACTION99
1.9339-2.03590.18691610.14282699X-RAY DIFFRACTION99
2.0359-2.16340.1791250.14752689X-RAY DIFFRACTION97
2.1634-2.33040.17211330.14372716X-RAY DIFFRACTION98
2.3304-2.56490.17161530.15192723X-RAY DIFFRACTION99
2.5649-2.9360.16211570.15942698X-RAY DIFFRACTION97
2.936-3.69870.15871440.14862786X-RAY DIFFRACTION99
3.6987-41.96240.16631640.14852826X-RAY DIFFRACTION97
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)
10.90970.1424-0.25013.135-1.39612.11080.05210.09960.0804-0.07090.16740.3258-0.1192-0.2362-0.22060.13650.00630.01360.17340.01920.190617.833631.305651.4785
21.5037-0.22490.20862.2774-0.44481.3250.0817-0.1572-0.13770.20490.05340.14490.0964-0.0752-0.14110.2135-0.02730.02010.17510.02890.13823.375416.693569.1338
35.6376-4.7883.84085.1577-5.24546.22950.31070.0397-0.3377-0.2514-0.01780.61710.3297-0.2034-0.27280.2539-0.0745-0.01370.21550.03260.280413.18939.583259.2743
41.0854-0.26280.12471.5134-0.38531.60080.05710.0703-0.1588-0.03880.01520.19430.1846-0.1499-0.07510.1581-0.0273-0.00220.15410.0140.196318.548814.492654.5803
53.8468-0.95781.45951.255-0.28071.80910.09520.1346-0.05840.0468-0.012-0.0540.11230.1435-0.09980.1396-0.0067-0.01240.0865-0.00290.120732.541515.715252.5333
62.0306-0.385-0.01881.3947-0.30240.88840.1202-0.1577-0.13340.1273-0.0362-0.03530.11470.0813-0.06130.1696-0.0183-0.02080.1614-0.00090.159334.304415.619260.3063
72.2666-0.68280.30061.6836-0.93671.94420.0833-0.01650.08640.117-0.038-0.0162-0.1720.069-0.03330.1764-0.02390.00330.1557-0.00930.139935.35728.840659.7036
81.1743-0.63811.00930.9878-0.89591.31360.0722-0.0129-0.05980.09510.00670.0235-0.00520.0055-0.08580.1574-0.0113-0.00650.15300.149536.332321.068458.3273
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 29:51 )A29 - 51
2X-RAY DIFFRACTION2( CHAIN A AND RESID 52:92 )A52 - 92
3X-RAY DIFFRACTION3( CHAIN A AND RESID 93:105 )A93 - 105
4X-RAY DIFFRACTION4( CHAIN A AND RESID 106:154 )A106 - 154
5X-RAY DIFFRACTION5( CHAIN A AND RESID 155:174 )A155 - 174
6X-RAY DIFFRACTION6( CHAIN A AND RESID 201:213 )A201 - 213
7X-RAY DIFFRACTION7( CHAIN A AND RESID 214:246 )A214 - 246
8X-RAY DIFFRACTION8( CHAIN A AND RESID 247:278 )A247 - 278

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