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- PDB-1bmq: CRYSTAL STRUCTURE OF THE COMPLEX OF INTERLEUKIN-1BETA CONVERTING ... -

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Entry
Database: PDB / ID: 1bmq
TitleCRYSTAL STRUCTURE OF THE COMPLEX OF INTERLEUKIN-1BETA CONVERTING ENZYME (ICE) WITH A PEPTIDE BASED INHIBITOR, (3S )-N-METHANESULFONYL-3-({1-[N-(2-NAPHTOYL)-L-VALYL]-L-PROLYL }AMINO)-4-OXOBUTANAMIDE
Components(PROTEIN (INTERLEUKIN-1 BETA CONVERTASE)) x 2
KeywordsHYDROLASE / CASPASE
Function / homology
Function and homology information


caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / NLRP1 inflammasome complex / cytokine precursor processing ...caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / NLRP1 inflammasome complex / cytokine precursor processing / canonical inflammasome complex / positive regulation of interleukin-18 production / NLRP3 inflammasome complex / caspase binding / CARD domain binding / osmosensory signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / Interleukin-1 processing / Interleukin-37 signaling / pattern recognition receptor signaling pathway / signaling receptor ligand precursor processing / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptotic inflammatory response / : / cytokine binding / cysteine-type endopeptidase activator activity involved in apoptotic process / The NLRP3 inflammasome / protein autoprocessing / protein maturation / Pyroptosis / Purinergic signaling in leishmaniasis infection / positive regulation of interleukin-1 beta production / NOD1/2 Signaling Pathway / kinase binding / cellular response to type II interferon / positive regulation of inflammatory response / cellular response to mechanical stimulus / SARS-CoV-1 activates/modulates innate immune responses / regulation of inflammatory response / cellular response to lipopolysaccharide / defense response to virus / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / endopeptidase activity / microtubule / defense response to bacterium / cysteine-type endopeptidase activity / nucleolus / apoptotic process / signal transduction / protein-containing complex / proteolysis / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 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
Chem-MNO / Caspase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.5 Å
AuthorsOkamoto, Y. / Anan, H. / Nakai, E. / Morihira, K. / Yonetoku, Y. / Kurihara, H. / Katayama, N. / Sakashita, H. / Terai, Y. / Takeuchi, M. ...Okamoto, Y. / Anan, H. / Nakai, E. / Morihira, K. / Yonetoku, Y. / Kurihara, H. / Katayama, N. / Sakashita, H. / Terai, Y. / Takeuchi, M. / Shibanuma, T. / Isomura, Y.
CitationJournal: Chem.Pharm.Bull. / Year: 1999
Title: Peptide based interleukin-1 beta converting enzyme (ICE) inhibitors: synthesis, structure activity relationships and crystallographic study of the ICE-inhibitor complex.
Authors: Okamoto, Y. / Anan, H. / Nakai, E. / Morihira, K. / Yonetoku, Y. / Kurihara, H. / Sakashita, H. / Terai, Y. / Takeuchi, M. / Shibanuma, T. / Isomura, Y.
History
DepositionJul 24, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 29, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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: PROTEIN (INTERLEUKIN-1 BETA CONVERTASE)
B: PROTEIN (INTERLEUKIN-1 BETA CONVERTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6143
Polymers29,0692
Non-polymers5451
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-36 kcal/mol
Surface area12860 Å2
MethodPISA
2
A: PROTEIN (INTERLEUKIN-1 BETA CONVERTASE)
B: PROTEIN (INTERLEUKIN-1 BETA CONVERTASE)
hetero molecules

A: PROTEIN (INTERLEUKIN-1 BETA CONVERTASE)
B: PROTEIN (INTERLEUKIN-1 BETA CONVERTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2286
Polymers58,1394
Non-polymers1,0892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area18090 Å2
ΔGint-88 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.700, 64.700, 161.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN (INTERLEUKIN-1 BETA CONVERTASE) / EC 3.4.22.26 / ICE / IL-1BETA CONVERTING ENZYME / CASPASE-1


Mass: 18810.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE INHIBITOR IS COVALENTLY ATTACHED TO THE SULPHUR ATOM OF CYSTEINE 285
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-3C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29466, caspase-1
#2: Protein PROTEIN (INTERLEUKIN-1 BETA CONVERTASE) / ICE


Mass: 10258.755 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE INHIBITOR IS COVALENTLY ATTACHED TO THE SULPHUR ATOM OF CYSTEINE 285
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-3C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29466, caspase-1
#3: Chemical ChemComp-MNO / (3S)-N-METHANESULFONYL-3-({1-[N-(2-NAPHTOYL)-L-VALYL]-L-PROLYL}AMINO)-4-OXOBUTANAMIDE


Mass: 544.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H32N4O7S
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: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 10-15% PEG 6000, 100MM HEPES PH 7.0
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
250 mMcitrate1drop
32.0 mMdithiothreitol1drop
415 %PEG40001reservoir
5400 mM1reservoirLi2SO4
6200 mMsodium HEPES1reservoir
75 mMsodium cacodylate1reservoir
80.5 %beta-octyl glucodside1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 15, 1997 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→60 Å / Num. obs: 15819 / % possible obs: 84.1 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
PROCESSdata reduction
PROCESSdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER
Starting model: 1ICE

1ice


Resolution: 2.5→8 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.317 1085 10 %RANDOM
Rwork0.233 ---
obs0.233 10838 89.7 %-
Displacement parametersBiso mean: 29 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 38 0 2070
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.771.5
X-RAY DIFFRACTIONx_mcangle_it2.882
X-RAY DIFFRACTIONx_scbond_it2.712
X-RAY DIFFRACTIONx_scangle_it4.232.5
LS refinement shellResolution: 2.5→2.65 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.382 144 9.7 %
Rwork0.341 1333 -
obs--75.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1MSI_XPLOR_PROTEIN_REP.PARMSI_XPLOR_TOPHCSDX.PRO
X-RAY DIFFRACTION2MNO.PARAMMNO.TOPH
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.5

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