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- PDB-1rwm: Crystal structure of human caspase-1 in complex with 4-oxo-3-[2-(... -

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Basic information

Entry
Database: PDB / ID: 1rwm
TitleCrystal structure of human caspase-1 in complex with 4-oxo-3-[2-(5-{[4-(quinoxalin-2-ylamino)-benzoylamino]-methyl}-thiophen-2-yl)-acetylamino]-pentanoic acid
Components(Interleukin-1 beta convertase) x 2
KeywordsHYDROLASE / protein-small molecule inhibitor complex
Function / homology
Function and homology information


aldose 1-epimerase activity / galactose catabolic process via UDP-galactose / glucose metabolic process / carbohydrate binding / DNA damage response
Similarity search - Function
Aldose 1-/Glucose-6-phosphate 1-epimerase / Aldose 1-epimerase / Caspase-like / Rossmann fold - #1460 / Glycoside hydrolase-type carbohydrate-binding / Galactose mutarotase-like domain superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-Q2Y / Uncharacterized protein YphB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRomanowski, M.J. / Waal, N.D. / Fahr, B.T. / O'Brien, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Structural analysis of caspase-1 inhibitors derived from Tethering.
Authors: O'Brien, T. / Fahr, B.T. / Sopko, M.M. / Lam, J.W. / Waal, N.D. / Raimundo, B.C. / Purkey, H.E. / Pham, P. / Romanowski, M.J.
History
DepositionDec 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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

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Assembly

Deposited unit
A: Interleukin-1 beta convertase
B: Interleukin-1 beta convertase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6603
Polymers30,1292
Non-polymers5321
Water1,24369
1
A: Interleukin-1 beta convertase
B: Interleukin-1 beta convertase
hetero molecules

A: Interleukin-1 beta convertase
B: Interleukin-1 beta convertase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3206
Polymers60,2574
Non-polymers1,0632
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area18460 Å2
ΔGint-102 kcal/mol
Surface area20900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.221, 63.221, 161.164
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsHeterotetramer (dimer of two heterodimers). Each heterodimer is represented by chains A (the p20 subunit) and B (the p10 subunit) of human caspase-1.

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Components

#1: Protein Interleukin-1 beta convertase / IL-1BC / IL-1 beta converting enzyme / ICE / Interleukin-1 beta converting enzyme / P45 / Caspase-1 / CASP-1


Mass: 19869.838 Da / Num. of mol.: 1 / Fragment: INTERLEUKIN-1 BETA CONVERTASE P20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon+ / References: UniProt: P29466, EC: 3.4.22.36
#2: Protein Interleukin-1 beta convertase / IL-1BC / IL-1 beta converting enzyme / ICE / Interleukin-1 beta converting enzyme / P45 / Caspase-1 / CASP-1


Mass: 10258.755 Da / Num. of mol.: 1 / Fragment: INTERLEUKIN-1 BETA CONVERTASE P10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon+ / References: UniProt: P29466, EC: 3.4.22.36
#3: Chemical ChemComp-Q2Y / 4-OXO-3-[2-(5-{[4-(QUINOXALIN-2-YLAMINO)-BENZOYLAMINO]-METHYL}-THIOPHEN-2-YL)-ACETYLAMINO]-PENTANOIC ACID


Mass: 531.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H25N5O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M PIPES, 200mM Li2SO4, 25% PEG2K MME, 10mM DTT, 3mM NaN3, 2mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 24, 2003
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 9552 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.128
Reflection shellResolution: 2.7→2.79 Å / Rmerge(I) obs: 0.382 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1ICE

1ice


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.877 / SU B: 13.025 / SU ML: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 3.18 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25437 437 4.7 %RANDOM
Rwork0.19934 ---
obs0.20191 8766 96.34 %-
all-9552 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.988 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å20 Å2
2--1.49 Å20 Å2
3----2.99 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 37 69 2175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212152
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1111.9662898
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0385259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021623
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1740.2976
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.892.51302
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.28452114
X-RAY DIFFRACTIONr_scbond_it1.7812.5850
X-RAY DIFFRACTIONr_scangle_it3.0245784
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.793 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.288 50
Rwork0.22 830

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