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- PDB-3rjm: CASPASE2 IN COMPLEX WITH CHDI LIGAND 33c -

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Basic information

Entry
Database: PDB / ID: 3rjm
TitleCASPASE2 IN COMPLEX WITH CHDI LIGAND 33c
Components
  • (Caspase-2) x 2
  • Peptide inhibitor (ACE)VDV(3PX)D-CHO
KeywordsHYDROLASE/HYDROLASE INHIBITOR / caspase-2 / p12 / p19 / caspase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


caspase-2 / endopeptidase complex / neural retina development / NADE modulates death signalling / luteolysis / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / 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 / luteolysis / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / 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
Peptide inhibitor (ACE)VDV(3PX)D-CHO / Caspase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsAbendroth, J. / Lorimer, D. / Stewart, L. / Maillard, M. / Kiselyov, A.S.
CitationJournal: Bioorg.Med.Chem. / Year: 2011
Title: Exploiting differences in caspase-2 and -3 S(2) subsites for selectivity: Structure-based design, solid-phase synthesis and in vitro activity of novel substrate-based caspase-2 inhibitors.
Authors: Maillard, M.C. / Brookfield, F.A. / Courtney, S.M. / Eustache, F.M. / Gemkow, M.J. / Handel, R.K. / Johnson, L.C. / Johnson, P.D. / Kerry, M.A. / Krieger, F. / Meniconi, M. / Munoz-Sanjuan, ...Authors: Maillard, M.C. / Brookfield, F.A. / Courtney, S.M. / Eustache, F.M. / Gemkow, M.J. / Handel, R.K. / Johnson, L.C. / Johnson, P.D. / Kerry, M.A. / Krieger, F. / Meniconi, M. / Munoz-Sanjuan, I. / Palfrey, J.J. / Park, H. / Schaertl, S. / Taylor, M.G. / Weddell, D. / Dominguez, C.
History
DepositionApr 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Sep 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 / 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 1.4Dec 6, 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-2
B: Caspase-2
C: Caspase-2
D: Caspase-2
E: Peptide inhibitor (ACE)VDV(3PX)D-CHO
F: Peptide inhibitor (ACE)VDV(3PX)D-CHO


Theoretical massNumber of molelcules
Total (without water)65,8866
Polymers65,8866
Non-polymers00
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17850 Å2
ΔGint-89 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.770, 97.380, 97.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A9 - 157
2114C9 - 157
1214A402 - 406
2214C402 - 406
1124B207 - 303
2124D207 - 303

NCS ensembles :
ID
1
2

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Components

#1: Protein Caspase-2 / / CASP-2 / Neural precursor cell expressed developmentally down-regulated protein 2 / NEDD-2 / ...CASP-2 / Neural precursor cell expressed developmentally down-regulated protein 2 / NEDD-2 / Protease ICH-1 / Caspase-2 subunit p18 / Caspase-2 subunit p13 / Caspase-2 subunit p12


Mass: 18992.535 Da / Num. of mol.: 2 / Fragment: Residues 167-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP2, Caspase-2, ICH1, NEDD2, p19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42575, caspase-2
#2: Protein Caspase-2 / / CASP-2 / Neural precursor cell expressed developmentally down-regulated protein 2 / NEDD-2 / ...CASP-2 / Neural precursor cell expressed developmentally down-regulated protein 2 / NEDD-2 / Protease ICH-1 / Caspase-2 subunit p18 / Caspase-2 subunit p13 / Caspase-2 subunit p12


Mass: 13336.546 Da / Num. of mol.: 2 / Fragment: Residues 348-452
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP2, Caspase-2, ICH1, NEDD2, p12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42575, caspase-2
#3: Protein/peptide Peptide inhibitor (ACE)VDV(3PX)D-CHO


Type: Peptide-like / Class: CASPASE inhibitor / Mass: 613.701 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: Peptide inhibitor (ACE)VDV(3PX)D-CHO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3246.98
2
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 26% PEG 3500, 100MM MES PH 6.5 - PH 7.0, SITTING DROP, VAPOR DIFFUSION, TEMPERATURE 290K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 15, 2010
RadiationMonochromator: RIGAKU VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 20552 / Num. obs: 20535 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 22.72 Å2 / Rmerge(I) obs: 0.157 / Net I/σ(I): 13.47
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1468 / % possible all: 100

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1pyo

1pyo


Resolution: 2.55→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.879 / SU B: 9.192 / SU ML: 0.204 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1040 5.1 %RANDOM
Rwork0.186 ---
all0.19 20535 --
obs0.19 20375 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4077 0 0 220 4297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214183
X-RAY DIFFRACTIONr_bond_other_d0.0010.022806
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.9615669
X-RAY DIFFRACTIONr_angle_other_deg0.8513.0016820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2245521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68523.586198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3915681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7851530
X-RAY DIFFRACTIONr_chiral_restr0.070.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214690
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02870
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_it0.581.52613
X-RAY DIFFRACTIONr_mcbond_other0.1071.51057
X-RAY DIFFRACTIONr_mcangle_it1.13524181
X-RAY DIFFRACTIONr_scbond_it1.5931568
X-RAY DIFFRACTIONr_scangle_it2.6484.51480
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1980medium positional0.310.5
22B1273medium positional0.270.5
11A1980medium thermal0.522
22B1273medium thermal0.532
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 81 -
Rwork0.215 1379 -
obs-1468 99.73 %

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