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- PDB-3qnw: Caspase-6 in complex with Z-VAD-FMK inhibitor -

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Basic information

Entry
Database: PDB / ID: 3qnw
TitleCaspase-6 in complex with Z-VAD-FMK inhibitor
Components
  • (Caspase-6) x 2
  • Z-VAD-FMK
KeywordsHYDROLASE/HYDROLASE INHIBITOR / cysteine protease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / positive regulation of necroptotic process / cellular response to staurosporine / : / : / TP53 Regulates Transcription of Caspase Activators and Caspases / hepatocyte apoptotic process / Apoptotic cleavage of cellular proteins ...caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / positive regulation of necroptotic process / cellular response to staurosporine / : / : / TP53 Regulates Transcription of Caspase Activators and Caspases / hepatocyte apoptotic process / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / intrinsic apoptotic signaling pathway by p53 class mediator / protein autoprocessing / Caspase-mediated cleavage of cytoskeletal proteins / cysteine-type peptidase activity / epithelial cell differentiation / activation of innate immune response / positive regulation of neuron apoptotic process / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / proteolysis / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Caspase-like / 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 ...Caspase-like / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide / Caspase-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMueller, I. / Lamers, M. / Ritchie, A. / Park, H. / Dominguez, C. / Munoz, I. / Maillard, M. / Kiselyov, A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Structure of human caspase-6 in complex with Z-VAD-FMK: New peptide binding mode observed for the non-canonical caspase conformation.
Authors: Muller, I. / Lamers, M.B. / Ritchie, A.J. / Dominguez, C. / Munoz-Sanjuan, I. / Kiselyov, A.
History
DepositionFeb 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Other
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
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
Revision 1.3Nov 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-6
B: Caspase-6
C: Caspase-6
D: Caspase-6
E: Caspase-6
F: Caspase-6
G: Caspase-6
H: Caspase-6
X: Z-VAD-FMK
Y: Z-VAD-FMK
Z: Z-VAD-FMK


Theoretical massNumber of molelcules
Total (without water)119,01111
Polymers119,01111
Non-polymers00
Water1,44180
1
A: Caspase-6
B: Caspase-6
C: Caspase-6
D: Caspase-6
E: Caspase-6
F: Caspase-6
G: Caspase-6
X: Z-VAD-FMK
Y: Z-VAD-FMK


Theoretical massNumber of molelcules
Total (without water)107,2399
Polymers107,2399
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Caspase-6
E: Caspase-6
F: Caspase-6
G: Caspase-6
H: Caspase-6
Z: Z-VAD-FMK


Theoretical massNumber of molelcules
Total (without water)77,3686
Polymers77,3686
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.206, 65.446, 91.718
Angle α, β, γ (deg.)90.00, 91.24, 90.00
Int Tables number4
Space group name H-MP1211
DetailsPROTEIN FORMS DIMERS OF DIMERS (CHAINS A/B AND C/D AND CHAINS E/F AND G/H). LIGAND DOES NOT BIND TO ALL HETERODIMERS

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Components

#1: Protein
Caspase-6 / CASP-6 / Apoptotic protease Mch-2 / Caspase-6 subunit p18 / Caspase-6 subunit p11


Mass: 18098.809 Da / Num. of mol.: 4 / Fragment: unp residues 24-179
Source method: isolated from a genetically manipulated source
Details: caspase-6 zymogen expressed in E.coli, mature caspase-6 via autoproteolysis
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP6, MCH2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P55212, caspase-6
#2: Protein
Caspase-6 / CASP-6 / Apoptotic protease Mch-2 / Caspase-6 subunit p18 / Caspase-6 subunit p11


Mass: 11300.012 Da / Num. of mol.: 4 / Fragment: unp residues 194-293
Source method: isolated from a genetically manipulated source
Details: caspase-6 zymogen expressed in E.coli, mature caspase-6 via autoproteolysis
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP6, MCH2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P55212, caspase-6
#3: Protein/peptide Z-VAD-FMK


Type: Peptide-like / Class: Inhibitor / Mass: 471.907 Da / Num. of mol.: 3 / Source method: obtained synthetically
References: N-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.3
Details: 0.1 M lithium sulfate, 0.1 M sodium citrate, 11% 2-propanol , VAPOR DIFFUSION, temperature 298K, pH 4.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.65→29.1 Å / Num. all: 30244 / Num. obs: 30002 / % possible obs: 99.2 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 14.8
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 3.6 / % possible all: 98.8

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.5.0110refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2wdp

2wdp


Resolution: 2.65→29.1 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.856 / SU B: 13.724 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R: 2.515 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28713 1505 5 %RANDOM
Rwork0.24038 ---
obs0.24275 28380 98.46 %-
all-28824 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.792 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å2-0.02 Å2
2---2.25 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.65→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6898 0 0 80 6978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0217065
X-RAY DIFFRACTIONr_bond_other_d0.0010.024664
X-RAY DIFFRACTIONr_angle_refined_deg0.8151.9439554
X-RAY DIFFRACTIONr_angle_other_deg0.7463.00111291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0045884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.76723.062307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3151080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6941536
X-RAY DIFFRACTIONr_chiral_restr0.0490.21057
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027970
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021587
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_it0.3531.54447
X-RAY DIFFRACTIONr_mcbond_other0.031.51823
X-RAY DIFFRACTIONr_mcangle_it0.65727048
X-RAY DIFFRACTIONr_scbond_it0.52832618
X-RAY DIFFRACTIONr_scangle_it0.8574.52503
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 102 -
Rwork0.286 2136 -
obs--98.63 %

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