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- PDB-3h1p: Mature Caspase-7 I213A with DEVD-CHO inhibitor bound to active site -

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Basic information

Entry
Database: PDB / ID: 3h1p
TitleMature Caspase-7 I213A with DEVD-CHO inhibitor bound to active site
Components
  • Caspase-7Caspase 7
  • N-ACETYL-L-ALPHA-ASPARTYL-L-ALPHA-GLUTAMYL-N-[(2S)-1-CARBOXY-3-HYDROXYPROPAN-2-YL]-L-VALINAMIDE
KeywordsHYDROLASE/INHIBITOR / protease / compensatory mechanism / apoptosis / cell death / cysteine protease / Thiol protease / Zymogen / HYDROLASE-INHIBITOR complex
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 / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cysteine-type endopeptidase activity involved in apoptotic process ...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 / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cysteine-type endopeptidase activity involved in apoptotic process / fibroblast apoptotic process / execution phase of apoptosis / Apoptotic cleavage of cellular proteins / protein maturation / Caspase-mediated cleavage of cytoskeletal proteins / cysteine-type peptidase activity / response to UV / striated muscle cell differentiation / protein catabolic process / protein processing / heart development / peptidase activity / neuron apoptotic process / cellular response to lipopolysaccharide / aspartic-type endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / proteolysis / extracellular space / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
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
Ac-Asp-Glu-Val-Asp-Aldehyde / Caspase-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.61 Å
AuthorsWitkowski, W.A. / Hardy, J.A.
CitationJournal: Protein Sci. / Year: 2009
Title: L2' loop is critical for caspase-7 active site formation.
Authors: Witkowski, W.A. / Hardy, J.A.
History
DepositionApr 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 5, 2011Group: Structure summary
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software
Revision 1.5Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details
Revision 1.6Sep 6, 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_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_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_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.7Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
C: N-ACETYL-L-ALPHA-ASPARTYL-L-ALPHA-GLUTAMYL-N-[(2S)-1-CARBOXY-3-HYDROXYPROPAN-2-YL]-L-VALINAMIDE
D: N-ACETYL-L-ALPHA-ASPARTYL-L-ALPHA-GLUTAMYL-N-[(2S)-1-CARBOXY-3-HYDROXYPROPAN-2-YL]-L-VALINAMIDE


Theoretical massNumber of molelcules
Total (without water)60,3484
Polymers60,3484
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-16 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.347, 89.347, 186.101
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-343-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 4 / Auth seq-ID: 60 - 300 / Label seq-ID: 11 - 251

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 29685.570 Da / Num. of mol.: 2 / Mutation: I213A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55210, caspase-7
#2: Protein/peptide N-ACETYL-L-ALPHA-ASPARTYL-L-ALPHA-GLUTAMYL-N-[(2S)-1-CARBOXY-3-HYDROXYPROPAN-2-YL]-L-VALINAMIDE


Type: Peptide-like / Class: Inhibitor / Mass: 488.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: Ac-Asp-Glu-Val-Asp-Aldehyde
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 3.61 Å3/Da / Density % sol: 65.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 14% PEG 3350, 300mM diammonium hydrogen citrate, 10mM guanidine hydrochloride, and 10mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 2, 2008 / Details: osmic mirror
RadiationMonochromator: Osmic Confocal Max-Flux / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. obs: 26471 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 0.694 Å2 / Rsym value: 0.083 / Net I/σ(I): 15.1
Reflection shellResolution: 2.61→2.7 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Num. unique all: 2587 / Rsym value: 0.694 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F1J

1f1j


Resolution: 2.61→40.26 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.418 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.342 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1328 5 %RANDOM
Rwork0.199 ---
obs0.202 26470 98.37 %-
all-2690 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.75 Å2 / Biso mean: 51.82 Å2 / Biso min: 20.34 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.3444 Å
Refinement stepCycle: LAST / Resolution: 2.61→40.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 0 119 3917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223875
X-RAY DIFFRACTIONr_angle_refined_deg1.8761.9495211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.415467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01224.513195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.86915687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7071520
X-RAY DIFFRACTIONr_chiral_restr0.1590.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022940
X-RAY DIFFRACTIONr_nbd_refined0.2790.21864
X-RAY DIFFRACTIONr_nbtor_refined0.3320.22577
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2241
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2770.22
X-RAY DIFFRACTIONr_mcbond_it1.5871.52387
X-RAY DIFFRACTIONr_mcangle_it2.77523771
X-RAY DIFFRACTIONr_scbond_it4.33731651
X-RAY DIFFRACTIONr_scangle_it6.5434.51440
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1803 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.410.5
MEDIUM THERMAL32
LS refinement shellResolution: 2.61→2.677 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 84 -
Rwork0.338 1821 -
all-1905 -
obs-2587 98.15 %

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