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- PDB-2h51: Crystal structure of human caspase-1 (Glu390->Asp and Arg286->Lys... -

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Basic information

Entry
Database: PDB / ID: 2h51
TitleCrystal structure of human caspase-1 (Glu390->Asp and Arg286->Lys) in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK)
Components
  • (Caspase-1) x 2
  • N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide
KeywordsHYDROLASE/HYDROLASE INHIBITOR / allosteric site / dimer interface / HYDROLASE / HYDROLASE-HYDROLASE 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
N-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide / Uncharacterized protein YphB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsScheer, J.M. / Wells, J.A. / Romanowski, M.J.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: An allosteric circuit in caspase-1.
Authors: Datta, D. / Scheer, J.M. / Romanowski, M.J. / Wells, J.A.
History
DepositionMay 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_comp_id / _struct_conn.ptnr2_auth_seq_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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 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: Caspase-1
B: Caspase-1
C: N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide


Theoretical massNumber of molelcules
Total (without water)30,5583
Polymers30,5583
Non-polymers00
Water3,873215
1
A: Caspase-1
B: Caspase-1
C: N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide

A: Caspase-1
B: Caspase-1
C: N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide


Theoretical massNumber of molelcules
Total (without water)61,1176
Polymers61,1176
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Buried area17340 Å2
ΔGint-103 kcal/mol
Surface area20280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.164, 63.164, 141.544
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-465-

HOH

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 Caspase-1


Mass: 19841.824 Da / Num. of mol.: 1 / Fragment: p20 subunit, residues 120-297 / Mutation: R286K
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(DE3) Codon+ / References: UniProt: P29466, EC: 3.4.22.36
#2: Protein Caspase-1


Mass: 10244.729 Da / Num. of mol.: 1 / Fragment: p10 subunit, residues 317-404 / Mutation: E390D
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(DE3) Codon+ / References: UniProt: P29466, EC: 3.4.22.36
#3: Protein/peptide N-[(benzyloxy)carbonyl]-L-valyl-N-[(2S)-1-carboxy-4-fluoro-3-oxobutan-2-yl]-L-alaninamide


Type: Peptide-like / Class: Inhibitor / Mass: 471.907 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: N-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M PIPES, 200 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, 2 mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.16 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2005 / Details: Rh coated bent cylindrical mirror
RadiationMonochromator: Double crystal, parallel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.16 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 16666 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 5
Reflection shellResolution: 2.1→2.17 Å / % possible all: 82.7

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
CrystalCleardata reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SC3

1sc3


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.907 / SU B: 4.468 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23632 834 5.1 %RANDOM
Rwork0.17959 ---
all0.214 16362 --
obs0.18232 15528 93.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.587 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 0 0 215 2256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212113
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0011.962848
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6355251
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_restr0.0690.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021560
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1830.21005
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2194
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7932.51272
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.98352074
X-RAY DIFFRACTIONr_scbond_it2.4482.5841
X-RAY DIFFRACTIONr_scangle_it3.6985773
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.173 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.227 70
Rwork0.196 1232
Refinement TLS params.Method: refined / Origin x: 60.2668 Å / Origin y: 48.2601 Å / Origin z: 32.0748 Å
111213212223313233
T0.0171 Å2-0.0118 Å2-0.0013 Å2-0.0419 Å2-0.0131 Å2--0.0308 Å2
L1.0544 °2-0.0089 °2-0.0886 °2-0.9673 °2-0.0965 °2--0.8846 °2
S-0.0121 Å °0.0977 Å °-0.0741 Å °-0.0405 Å °0.0119 Å °0.034 Å °0.0915 Å °-0.1617 Å °0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA128 - 1459 - 26
2X-RAY DIFFRACTION1AA149 - 29730 - 178
3X-RAY DIFFRACTION1BB318 - 4042 - 88
4X-RAY DIFFRACTION1AC5011

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