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- PDB-7paw: MALT1 in complex with compound 1 -

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Basic information

Entry
Database: PDB / ID: 7paw
TitleMALT1 in complex with compound 1
ComponentsMucosa-associated lymphoid tissue lymphoma translocation protein 1
KeywordsTRANSFERASE / Paracaspase / inhibitor complex / CBM 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
Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / MALT1, death domain / MALT1 immunoglobulin-like domain / MALT1 Ig-like domain / Immunoglobulin domain / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily ...Mucosa-associated lymphoid tissue lymphoma translocation protein 1 / MALT1, death domain / MALT1 immunoglobulin-like domain / MALT1 Ig-like domain / 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
Similarity search - Domain/homology
Chem-6IT / Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsKack, H. / Oster, L.
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: Discovery and optimization of cyclohexane-1,4-diamines as allosteric MALT1 inhibitors.
Authors: Schiesser, S. / Hajek, P. / Pople, H.E. / Kack, H. / Oster, L. / Cox, R.J.
History
DepositionJul 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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


Theoretical massNumber of molelcules
Total (without water)88,7533
Polymers88,3402
Non-polymers4131
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-15 kcal/mol
Surface area31010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.450, 74.970, 106.870
Angle α, β, γ (deg.)90.000, 93.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 44169.918 Da / Num. of mol.: 2 / Mutation: D595K, S617K, H666A, H681E
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-6IT / ~{N}1-(3-chloranyl-[1,2,4]triazolo[4,3-b]pyridazin-6-yl)-~{N}4-[2-(trifluoromethyl)pyrimidin-4-yl]cyclohexane-1,4-diamine


Mass: 412.800 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16ClF3N8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Tris, PEG3350, sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.19→53.6 Å / Num. obs: 30539 / % possible obs: 71.9 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.041 / Net I/σ(I): 13.6
Reflection shellResolution: 2.19→2.29 Å / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1527 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.27data extraction
autoPROC1.1.7data reduction
autoPROC1.1.7data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UOA

3uoa


Resolution: 2.19→53.31 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.902 / SU R Cruickshank DPI: 0.421 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.384 / SU Rfree Blow DPI: 0.239 / SU Rfree Cruickshank DPI: 0.248
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1571 5.14 %RANDOM
Rwork0.2 ---
obs0.202 30539 71.9 %-
Displacement parametersBiso max: 158.8 Å2 / Biso mean: 55.94 Å2 / Biso min: 13.53 Å2
Baniso -1Baniso -2Baniso -3
1--3.3124 Å20 Å2-3.544 Å2
2--4.887 Å20 Å2
3----1.5746 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.19→53.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5640 0 28 50 5718
Biso mean--52.99 35.98 -
Num. residues----713
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2069SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes967HARMONIC5
X-RAY DIFFRACTIONt_it5766HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion741SEMIHARMONIC5
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_contact6385SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5766HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7781HARMONIC21.18
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion20.84
LS refinement shellResolution: 2.19→2.24 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2513 35 5.73 %
Rwork0.218 576 -
all0.2199 611 -
obs--25.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9450.08161.8540.7233-0.1313.92310.0578-0.7407-0.12650.11540.007-0.08740.00090.125-0.0648-0.3276-0.059-0.01820.07810.0143-0.268231.22-3.282840.3722
23.43510.25462.33881.8621-0.86324.2867-0.07840.2596-0.0468-0.3730.10060.14550.1464-0.0911-0.0221-0.2155-0.0215-0.0342-0.33070.0049-0.18753.50840.9335-1.3062
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A338 - 720
2X-RAY DIFFRACTION2{ B|* }B338 - 717

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