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- PDB-3od5: Crystal structure of active caspase-6 bound with Ac-VEID-CHO -

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Basic information

Entry
Database: PDB / ID: 3od5
TitleCrystal structure of active caspase-6 bound with Ac-VEID-CHO
Components
  • Caspase-6
  • peptide aldehyde inhibitor AC-VEID-CHO
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Caspase domain / Apoptotic 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
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
N-acetyl-L-valyl-L-alpha-glutamyl-N-[(2S)-1-carboxy-3-oxopropan-2-yl]-L-isoleucinamide / CACODYLATE ION / Caspase-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWang, X.-J. / Liu, X. / Wang, K.-T. / Cao, Q. / Su, X.-D.
CitationJournal: Embo Rep. / Year: 2010
Title: Crystal structures of human caspase 6 reveal a new mechanism for intramolecular cleavage self-activation
Authors: Wang, X.-J. / Cao, Q. / Liu, X. / Wang, K.-T. / Mi, W. / Zhang, Y. / Li, L.-F. / Leblanc, A.C. / Su, X.-D.
History
DepositionAug 11, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-6
C: peptide aldehyde inhibitor AC-VEID-CHO
B: Caspase-6
D: peptide aldehyde inhibitor AC-VEID-CHO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,17412
Polymers65,0784
Non-polymers1,0968
Water13,745763
1
A: Caspase-6
C: peptide aldehyde inhibitor AC-VEID-CHO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0876
Polymers32,5392
Non-polymers5484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-3 kcal/mol
Surface area11790 Å2
MethodPISA
2
B: Caspase-6
D: peptide aldehyde inhibitor AC-VEID-CHO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0876
Polymers32,5392
Non-polymers5484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-2 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.464, 89.589, 61.145
Angle α, β, γ (deg.)90.00, 111.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 32054.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: delta-prodomain; Caspase-6 subunit p18/Caspase-6 subunit p11
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P55212, caspase-6
#2: Protein/peptide peptide aldehyde inhibitor AC-VEID-CHO


Type: Polypeptide / Class: Inhibitor / Mass: 484.543 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: ligand molecule synthesized
References: N-acetyl-L-valyl-L-alpha-glutamyl-N-[(2S)-1-carboxy-3-oxopropan-2-yl]-L-isoleucinamide
#3: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 763 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsADDING DTT DURING CRYSTALLIZATION, CACODYLATE IN THE CRYSTALLIZATION BUFFER WAS REDUCED TO (CH3)2AS ...ADDING DTT DURING CRYSTALLIZATION, CACODYLATE IN THE CRYSTALLIZATION BUFFER WAS REDUCED TO (CH3)2AS AND BOUND TO THE RESIDES CYS 163 OF THE PROTEIN.

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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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% w/v PEG 8000, 0.2M magnesium acetate, 0.1M sodium cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 73391 / Num. obs: 68657 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 10.65 Å2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NR2

3nr2


Resolution: 1.6→35.178 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.901 / SU ML: 0.17 / σ(F): 0.13 / Phase error: 17.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1893 2793 4.11 %RANDOM
Rwork0.1551 65242 --
obs0.1565 68035 93.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.851 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso max: 86.15 Å2 / Biso mean: 19.9399 Å2 / Biso min: 3.91 Å2
Baniso -1Baniso -2Baniso -3
1--6.3185 Å2-0 Å21.8968 Å2
2---0.2238 Å20 Å2
3----4.5502 Å2
Refinement stepCycle: LAST / Resolution: 1.6→35.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3901 0 24 763 4688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154009
X-RAY DIFFRACTIONf_angle_d1.5475393
X-RAY DIFFRACTIONf_dihedral_angle_d15.8041427
X-RAY DIFFRACTIONf_chiral_restr0.127585
X-RAY DIFFRACTIONf_plane_restr0.008689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62760.26791200.21582901X-RAY DIFFRACTION83
1.6276-1.65720.25821350.20422983X-RAY DIFFRACTION85
1.6572-1.68910.22671200.19443048X-RAY DIFFRACTION86
1.6891-1.72350.21011300.18643055X-RAY DIFFRACTION87
1.7235-1.7610.20821330.18093079X-RAY DIFFRACTION89
1.761-1.8020.22441370.16573136X-RAY DIFFRACTION90
1.802-1.8470.20821360.15283175X-RAY DIFFRACTION91
1.847-1.8970.16431380.14753101X-RAY DIFFRACTION89
1.897-1.95280.1891390.15383333X-RAY DIFFRACTION95
1.9528-2.01580.20231400.14753290X-RAY DIFFRACTION94
2.0158-2.08790.18951480.14173345X-RAY DIFFRACTION96
2.0879-2.17140.18541470.143400X-RAY DIFFRACTION96
2.1714-2.27020.1981430.14713355X-RAY DIFFRACTION96
2.2702-2.38990.17821440.14713347X-RAY DIFFRACTION96
2.3899-2.53960.19051450.14453429X-RAY DIFFRACTION97
2.5396-2.73560.16011460.14363408X-RAY DIFFRACTION98
2.7356-3.01080.16841490.14783470X-RAY DIFFRACTION98
3.0108-3.44610.17581470.14953475X-RAY DIFFRACTION98
3.4461-4.34050.16381480.13023457X-RAY DIFFRACTION98
4.3405-35.18650.16861480.14763455X-RAY DIFFRACTION97

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