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- PDB-1shl: CASPASE-7 IN COMPLEX WITH FICA ALLOSTERIC INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1shl
TitleCASPASE-7 IN COMPLEX WITH FICA ALLOSTERIC INHIBITOR
ComponentsCaspase-7
KeywordsHYDROLASE / caspase / protease / cysteine protease / allosteric / central-cavity / dimer interface / inhibitor
Function / homology
Function and homology information


caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes ...caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / execution phase of apoptosis / Apoptotic cleavage of cellular proteins / protein maturation / Caspase-mediated cleavage of cytoskeletal proteins / response to UV / cysteine-type peptidase activity / striated muscle cell differentiation / protein catabolic process / protein processing / positive regulation of neuron apoptotic process / peptidase activity / heart development / cellular response to lipopolysaccharide / neuron apoptotic process / aspartic-type endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / proteolysis / RNA binding / extracellular space / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Rossmann fold - #1460 / 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 ...Rossmann fold - #1460 / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FXN / Caspase-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å
AuthorsHardy, J.A. / Lam, J. / Nguyen, J.T. / O'Brien, T. / Wells, J.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Discovery of an allosteric site in the caspases
Authors: Hardy, J.A. / Lam, J. / Nguyen, J.T. / O'Brien, T. / Wells, J.A.
History
DepositionFeb 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-7
B: Caspase-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7134
Polymers56,2362
Non-polymers4772
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-15 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.220, 90.220, 186.621
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNASNASN4AA59 - 1483 - 92
21GLNGLNASNASN4BB59 - 1483 - 92
32VALVALGLNGLN4AA149 - 18493 - 128
42VALVALGLNGLN4BB149 - 18493 - 128
53ASPASPTHRTHR6AA218 - 225152 - 159
63ASPASPTHRTHR6BB218 - 225152 - 159
74SERSERARGARG4AA239 - 271173 - 205
84SERSERARGARG4BB239 - 271173 - 205
95ILEILEGLNGLN4AA288 - 303222 - 237
105ILEILEGLNGLN4BB288 - 303222 - 237

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Components

#1: Protein Caspase-7 / ICE-like apoptotic protease 3 / ICE-LAP3 / Apoptotic protease Mch-3 / CMH-1


Mass: 28118.074 Da / Num. of mol.: 2 / Mutation: D192A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Caspase-7 large and small subunits were co-expressed from two separate plasmids , yielding a large subunit of residues 57-199 and a small subunit of residues 21 0-303 with the addition ...Description: Caspase-7 large and small subunits were co-expressed from two separate plasmids , yielding a large subunit of residues 57-199 and a small subunit of residues 21 0-303 with the addition of eight amino acids QLHHHHHH.
Gene: CASP7, MCH3 / Plasmid: pJH07, pJH08 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P55210, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-FXN / 5-FLUORO-1H-INDOLE-2-CARBOXYLIC ACID-(2-MERCAPTO-ETHYL)-AMIDE / FICA


Mass: 238.281 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11FN2OS

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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: 3.9 Å3/Da / Density % sol: 68.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: citrate, lithium sulfate, sodium chloride, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.8856 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 7, 2003 / Details: beamline 9-1 standard
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 3→21.7 Å / Num. obs: 18022 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 75.82 Å2 / Rsym value: 0.076 / Net I/σ(I): 7.89
Reflection shellResolution: 3→3.08 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 1286 / Rsym value: 0.46 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1K88

1k88


Resolution: 3→10 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.879 / SU B: 15.338 / SU ML: 0.274 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.611 / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27327 897 5.1 %RANDOM
Rwork0.2211 ---
all0.22362 17536 --
obs0.2236 16639 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.095 Å2
Baniso -1Baniso -2Baniso -3
1-3.45 Å21.73 Å20 Å2
2--3.45 Å20 Å2
3----5.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.366 Å0.611 Å
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 0 32 0 3196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223243
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.964356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.995390
X-RAY DIFFRACTIONr_chiral_restr0.0860.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022414
X-RAY DIFFRACTIONr_nbd_refined0.2220.21321
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.23
X-RAY DIFFRACTIONr_mcbond_it2.162.51967
X-RAY DIFFRACTIONr_mcangle_it3.82953159
X-RAY DIFFRACTIONr_scbond_it2.2262.51276
X-RAY DIFFRACTIONr_scangle_it3.50351197
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1382medium positional0.460.5
68loose positional0.565
1382medium thermal0.772
68loose thermal3.3410
LS refinement shellResolution: 3→3.095 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.325 88
Rwork0.295 1505

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