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- PDB-3r6l: Caspase-2 T380A bound with Ac-VDVAD-CHO -

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Basic information

Entry
Database: PDB / ID: 3r6l
TitleCaspase-2 T380A bound with Ac-VDVAD-CHO
Components
  • Caspase-2 subunit p12
  • Caspase-2 subunit p18
  • Peptide Inhibitor (ACE)VDVAD-CHO
KeywordsHYDROLASE/HYDROLASE INHIBITOR / hydrolase / apoptosis / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


caspase-2 / endopeptidase complex / neural retina development / NADE modulates death signalling / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / luteolysis / cysteine-type endopeptidase activity involved in execution phase of apoptosis / execution phase of apoptosis / TP53 Regulates Transcription of Caspase Activators and Caspases / ectopic germ cell programmed cell death ...caspase-2 / endopeptidase complex / neural retina development / NADE modulates death signalling / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / luteolysis / cysteine-type endopeptidase activity involved in execution phase of apoptosis / execution phase of apoptosis / TP53 Regulates Transcription of Caspase Activators and Caspases / ectopic germ cell programmed cell death / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / apoptotic signaling pathway / NOD1/2 Signaling Pathway / protein processing / cellular response to mechanical stimulus / positive regulation of neuron apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of apoptotic process / protein domain specific binding / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / nucleolus / negative regulation of apoptotic process / enzyme binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Caspase-2 / Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 ...Caspase-2 / Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment 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 / Death-like domain superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyl-L-valyl-L-alpha-aspartyl-L-valyl-N-[(2R)-1-carboxy-3-oxopropan-2-yl]-L-alaninamide / Caspase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTang, Y. / Wells, J. / Arkin, M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and enzymatic insights into caspase-2 protein substrate recognition and catalysis.
Authors: Tang, Y. / Wells, J.A. / Arkin, M.R.
History
DepositionMar 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Dec 12, 2012Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-2 subunit p18
B: Caspase-2 subunit p12
C: Caspase-2 subunit p18
D: Caspase-2 subunit p12
F: Peptide Inhibitor (ACE)VDVAD-CHO
E: Peptide Inhibitor (ACE)VDVAD-CHO


Theoretical massNumber of molelcules
Total (without water)63,0246
Polymers63,0246
Non-polymers00
Water7,332407
1
A: Caspase-2 subunit p18
B: Caspase-2 subunit p12
E: Peptide Inhibitor (ACE)VDVAD-CHO


Theoretical massNumber of molelcules
Total (without water)31,5123
Polymers31,5123
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-36 kcal/mol
Surface area12260 Å2
MethodPISA
2
C: Caspase-2 subunit p18
D: Caspase-2 subunit p12
F: Peptide Inhibitor (ACE)VDVAD-CHO


Theoretical massNumber of molelcules
Total (without water)31,5123
Polymers31,5123
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-37 kcal/mol
Surface area12460 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17710 Å2
ΔGint-91 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.912, 97.063, 98.257
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Caspase-2 subunit p18 /


Mass: 18093.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP2, ICH1, NEDD2 / Production host: Escherichia coli (E. coli)
References: UniProt: P42575, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Caspase-2 subunit p12 /


Mass: 12891.013 Da / Num. of mol.: 2 / Mutation: T380A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP2, ICH1, NEDD2 / Production host: Escherichia coli (E. coli)
References: UniProt: P42575, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#3: Protein/peptide Peptide Inhibitor (ACE)VDVAD-CHO


Type: Peptide-like / Class: Inhibitor / Mass: 527.568 Da / Num. of mol.: 2 / Source method: obtained synthetically
References: N-acetyl-L-valyl-L-alpha-aspartyl-L-valyl-N-[(2R)-1-carboxy-3-oxopropan-2-yl]-L-alaninamide
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE ARE NO LINKS BETWEEN CYS 320 AND CHAINS E,F

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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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 15% PEG 3350, 3mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2009
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 47911 / Num. obs: 47911 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.9→1.93 Å / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.46 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19398 2408 5 %RANDOM
Rwork0.16846 ---
obs0.16978 45304 99.45 %-
all-47911 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.101 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å2-0 Å2-0 Å2
2---0.42 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4054 0 0 407 4461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224172
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.391.9575647
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.665529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65723.789190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9415705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0051526
X-RAY DIFFRACTIONr_chiral_restr0.0960.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213164
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8971.52614
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72524186
X-RAY DIFFRACTIONr_scbond_it2.6131558
X-RAY DIFFRACTIONr_scangle_it4.3014.51453
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 148 -
Rwork0.195 3207 -
obs--96.33 %

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