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- PDB-4i1r: Human MALT1 (caspase-IG3) in complex with thioridazine -

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Basic information

Entry
Database: PDB / ID: 4i1r
TitleHuman MALT1 (caspase-IG3) in complex with thioridazine
ComponentsMucosa-associated lymphoid tissue lymphoma translocation protein 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


polkadots / B-1 B cell differentiation / positive regulation of T-helper 17 cell differentiation / CBM complex / regulation of T cell receptor signaling pathway / response to fungus / activation of NF-kappaB-inducing kinase activity / CLEC7A/inflammasome pathway / nuclear export / B cell activation ...polkadots / B-1 B cell differentiation / positive regulation of T-helper 17 cell differentiation / CBM complex / regulation of T cell receptor signaling pathway / response to fungus / activation of NF-kappaB-inducing kinase activity / CLEC7A/inflammasome pathway / nuclear export / B cell activation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / small molecule binding / T cell proliferation / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-2 production / proteolysis involved in protein catabolic process / positive regulation of interleukin-1 beta production / positive regulation of protein ubiquitination / Activation of NF-kappaB in B cells / positive regulation of T cell cytokine production / CLEC7A (Dectin-1) signaling / fibrillar center / defense response / FCERI mediated NF-kB activation / ubiquitin-protein transferase activity / : / Downstream TCR signaling / peptidase activity / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / protease binding / endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / innate immune response / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein-containing complex / proteolysis / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Immunoglobulin-like - #3360 / Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / MALT1, death domain / MALT1 immunoglobulin-like domain / MALT1 Ig-like domain / Rossmann fold - #1460 / Immunoglobulin domain / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : ...Immunoglobulin-like - #3360 / Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / MALT1, death domain / MALT1 immunoglobulin-like domain / MALT1 Ig-like domain / Rossmann fold - #1460 / Immunoglobulin domain / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Immunoglobulin domain / Death-like domain superfamily / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-LZU / Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSchlauderer, F. / Lammens, K. / Hopfner, K.P.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Structural Analysis of Phenothiazine Derivatives as Allosteric Inhibitors of the MALT1 Paracaspase.
Authors: Schlauderer, F. / Lammens, K. / Nagel, D. / Vincendeau, M. / Eitelhuber, A.C. / Verhelst, S.H. / Kling, D. / Chrusciel, A. / Ruland, J. / Krappmann, D. / Hopfner, K.P.
History
DepositionNov 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5602
Polymers44,1901
Non-polymers3711
Water46826
1
A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
hetero molecules

A: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1214
Polymers88,3802
Non-polymers7412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)94.838, 70.608, 57.525
Angle α, β, γ (deg.)90.00, 93.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / MALT lymphoma-associated translocation / Paracaspase


Mass: 44189.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MALT1, MLT / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UDY8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-LZU / 10-{2-[(2S)-1-methylpiperidin-2-yl]ethyl}-2-(methylsulfanyl)-10H-phenothiazine / Thioridazine


Mass: 370.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26N2S2 / Comment: antipsychotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 200 M magnesium formate, 13 % PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 2.7→41.09 Å / Num. obs: 1667 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 86.51 Å2
Reflection shellResolution: 2.7→2.85 Å / % possible all: 97.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
PHASERphasing
BUSTER2.11.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→41.09 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.913 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1020 9.82 %RANDOM
Rwork0.201 ---
obs0.205 10386 98.8 %-
Displacement parametersBiso mean: 105.17 Å2
Baniso -1Baniso -2Baniso -3
1-6.4007 Å20 Å219.8237 Å2
2---11.7734 Å20 Å2
3---5.3727 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: LAST / Resolution: 2.7→41.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2803 0 25 26 2854
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092884HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.233894HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1034SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes401HARMONIC5
X-RAY DIFFRACTIONt_it2884HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion23.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion365SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3226SEMIHARMONIC4
LS refinement shellResolution: 2.7→3.02 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3179 296 10.11 %
Rwork0.2373 2632 -
all0.2454 2928 -
obs--98.8 %
Refinement TLS params.Method: refined / Origin x: -21.3496 Å / Origin y: -17.6955 Å / Origin z: 8.9455 Å
111213212223313233
T-0.1141 Å20.0862 Å2-0.0839 Å2-0.0145 Å2-0.061 Å2---0.133 Å2
L3.2439 °21.4195 °22.7563 °2-1.3351 °20.5081 °2--3.901 °2
S0.0573 Å °0.0417 Å °0.1411 Å °-0.0406 Å °-0.0541 Å °0.1228 Å °-0.1108 Å °0.0268 Å °-0.0032 Å °
Refinement TLS groupSelection details: { A|338 - A|720 }

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