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- PDB-9mkd: Crystal structure of MALT1 in complex with an allosteric inhibitor -

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Basic information

Entry
Database: PDB / ID: 9mkd
TitleCrystal structure of MALT1 in complex with an allosteric inhibitor
ComponentsMucosa-associated lymphoid tissue lymphoma translocation protein 1
KeywordsHYDROLASE / ALLOSTERIC INHIBITOR
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 / CLEC7A/inflammasome pathway / nuclear export / small molecule binding / 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 / CLEC7A/inflammasome pathway / nuclear export / small molecule binding / B cell activation / endopeptidase activator activity / T cell proliferation / positive regulation of interleukin-2 production / proteolysis involved in protein catabolic process / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-1 beta production / positive regulation of protein ubiquitination / Activation of NF-kappaB in B cells / defense response / positive regulation of T cell cytokine production / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / fibrillar center / ubiquitin-protein transferase activity / Downstream TCR signaling / peptidase activity / T cell receptor signaling pathway / protease binding / regulation of apoptotic process / endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / positive regulation of canonical NF-kappaB signal transduction / innate immune response / cysteine-type endopeptidase activity / 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 ...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
: / TRIETHYLENE GLYCOL / Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsBell, J.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Accelerated In Silico Discovery of SGR-1505 : A Potent MALT1 Allosteric Inhibitor for the Treatment of Mature B-Cell Malignancies.
Authors: Nie, Z. / Trzoss, M. / Placzek, A.T. / Trzoss, L. / Krilov, G. / Feng, S. / Lawrenz, M. / Ye, M. / Marshall, N. / Dingley, K.H. / Pelletier, R.D. / Lai, W.G. / Bell, J.A. / Tang, H. / ...Authors: Nie, Z. / Trzoss, M. / Placzek, A.T. / Trzoss, L. / Krilov, G. / Feng, S. / Lawrenz, M. / Ye, M. / Marshall, N. / Dingley, K.H. / Pelletier, R.D. / Lai, W.G. / Bell, J.A. / Tang, H. / Devine, P. / Liu, Z. / Skrdla, P. / Shimanovich, R. / Liu, M. / Wang, R. / Xu, X. / Abel, R. / Akinsanya, K. / Yin, W.
History
DepositionDec 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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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)89,02416
Polymers87,5452
Non-polymers1,48014
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.910, 76.970, 92.270
Angle α, β, γ (deg.)90.00, 93.42, 90.00
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: 43772.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MALT1, MLT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UDY8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-A1BMX / (9R)-2-chloro-N-[5-chloro-6-(2H-1,2,3-triazol-2-yl)pyridin-3-yl]-8,8-dimethyl-7,8-dihydro-6H-pyrazolo[1,5-a]pyrrolo[2,3-e]pyrimidine-6-carboxamide


Mass: 444.277 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H15Cl2N9O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.10 M sodium hepes, 0.40 M calcium chloride 20% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.45→34.56 Å / Num. obs: 37685 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.042 / Rrim(I) all: 0.079 / Net I/σ(I): 10
Reflection shellResolution: 2.45→2.55 Å / Rmerge(I) obs: 0.453 / Num. unique obs: 4245 / CC1/2: 0.875 / Rpim(I) all: 0.28 / Rrim(I) all: 0.534

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Processing

Software
NameVersionClassification
PRIME-Xrefinement
DIALS1.14.8data reduction
Aimless0.7.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→34.56 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1768 4.7 %RANDOM
Rwork0.211 ---
obs-37667 99.9 %-
Solvent computationBsol: 64.88 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso mean: 56.75 Å2
Baniso -1Baniso -2Baniso -3
1--8.049 Å20 Å215.082 Å2
2---1.286 Å20 Å2
3---9.335 Å2
Refinement stepCycle: LAST / Resolution: 2.45→34.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5838 0 81 246 6165
Refine LS restraintsType: OPLS 2005X
LS refinement shellResolution: 2.45→2.54 Å
RfactorNum. reflection% reflection
Rfree0.386 184 4.9 %
Rwork0.298 3766 -
obs--100 %

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