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- PDB-38go: Crystal structure of MALT1 in complex with safimaltib -

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Basic information

Entry
Database: PDB / ID: 38go
TitleCrystal structure of MALT1 in complex with safimaltib
ComponentsMucosa-associated lymphoid tissue lymphoma translocation protein 1
KeywordsHYDROLASE / protease / inhibitor / paracaspase / allosteric
Function / homology
Function and homology information


polkadots / positive regulation of T-helper 17 cell differentiation / CBM complex / CLEC7A/inflammasome pathway / nuclear export / regulation of canonical NF-kappaB signal transduction / small molecule binding / lipopolysaccharide-mediated signaling pathway / B cell activation / endopeptidase activator activity ...polkadots / positive regulation of T-helper 17 cell differentiation / CBM complex / CLEC7A/inflammasome pathway / nuclear export / regulation of canonical NF-kappaB signal transduction / small molecule binding / lipopolysaccharide-mediated signaling pathway / B cell activation / endopeptidase activator activity / positive regulation of interleukin-2 production / : / positive regulation of protein ubiquitination / positive regulation of interleukin-1 beta production / defense response / positive regulation of T cell cytokine production / Activation of NF-kappaB in B cells / T cell receptor signaling pathway / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / ubiquitin-protein transferase activity / peptidase activity / Downstream TCR signaling / protease binding / endopeptidase activity / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / innate immune response / cysteine-type endopeptidase activity / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein-containing complex / proteolysis / identical protein binding / nucleus / cytosol / cytoplasm
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
: / Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsXu, R. / Grant, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Preclinical characterization of the potent and selective MALT1 inhibitor safimaltib in B cell lymphoma models
Authors: Philippar, U. / Lu, T. / Fontan, L. / Xia, M. / Vloemans, N. / Bekkers, M. / Gaudiano, M. / Irrechukwu, O. / van den Biggelaar, D. / Perova, T. / Guimerans-Lorenzo, I. / Wnuk-Lipinska, K. / ...Authors: Philippar, U. / Lu, T. / Fontan, L. / Xia, M. / Vloemans, N. / Bekkers, M. / Gaudiano, M. / Irrechukwu, O. / van den Biggelaar, D. / Perova, T. / Guimerans-Lorenzo, I. / Wnuk-Lipinska, K. / Cornelissen, I. / Van Heerden, M. / Van Der Leede, B. / Amssoms, K. / Xu, R. / Grant, J. / Trella, E. / Abraham, Y. / Kimpe, K. / Medaer, B. / Greway, T. / Snoeys, J. / Jacobs, F. / Cummings, M.D. / Sun, W. / Thuring, J.W. / Wu, T. / Gaj, S. / Verbist, B. / Connolly, P.J. / Austin, N. / Balasubramanian, S. / Kinyamu-Akunda, J. / Packman, K. / Edwards, J.P. / Elsayed, Y. / Fourneau, N. / Morschhauser, F. / Gerecitano, J. / Bussolari, J. / Melnick, A. / Attar, R.
History
DepositionAug 25, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)89,7979
Polymers88,4882
Non-polymers1,3097
Water3,891216
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)89,85910
Polymers88,4882
Non-polymers1,3718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2
B: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)89,7358
Polymers88,4882
Non-polymers1,2476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)144.451, 66.664, 94.444
Angle α, β, γ (deg.)90.000, 126.647, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 44243.820 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-A1DY2 / (1M)-1-(1-oxo-1,2-dihydroisoquinolin-5-yl)-5-(trifluoromethyl)-N-[2-(trifluoromethyl)pyridin-4-yl]-1H-pyrazole-4-carboxamide


Mass: 467.324 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H11F6N5O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.06 Å3/Da / Density % sol: 40.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 29% PEG3350, 5mM DTT, 0.2M MgCl2, 0.1M BIS-TRIS, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.00001 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.07→57.79 Å / Num. obs: 44040 / % possible obs: 99.8 % / Redundancy: 20 % / Biso Wilson estimate: 42.06 Å2 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.04 / Net I/σ(I): 9.9
Reflection shellResolution: 2.07→2.1 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.341 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2089 / Rpim(I) all: 0.876 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→57.79 Å / SU ML: 0.2691 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5617
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2337 2175 4.95 %
Rwork0.1918 41780 -
obs0.1938 43955 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.85 Å2
Refinement stepCycle: LAST / Resolution: 2.07→57.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5466 0 86 216 5768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00595660
X-RAY DIFFRACTIONf_angle_d0.83327662
X-RAY DIFFRACTIONf_chiral_restr0.0473868
X-RAY DIFFRACTIONf_plane_restr0.0046989
X-RAY DIFFRACTIONf_dihedral_angle_d21.11822109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.110.37341270.33062477X-RAY DIFFRACTION95.56
2.11-2.160.27681340.27582596X-RAY DIFFRACTION99.42
2.16-2.220.25361340.22782623X-RAY DIFFRACTION99.78
2.22-2.280.30311670.22472565X-RAY DIFFRACTION99.74
2.28-2.340.28711400.21792578X-RAY DIFFRACTION99.74
2.34-2.420.29951350.20762613X-RAY DIFFRACTION99.85
2.42-2.510.28861320.20882586X-RAY DIFFRACTION99.89
2.51-2.610.29321330.21282598X-RAY DIFFRACTION99.96
2.61-2.730.26061410.20982643X-RAY DIFFRACTION100
2.73-2.870.27521390.20562618X-RAY DIFFRACTION100
2.87-3.050.29261210.20682641X-RAY DIFFRACTION99.89
3.05-3.280.26311080.19212635X-RAY DIFFRACTION100
3.28-3.610.18681480.16852640X-RAY DIFFRACTION99.89
3.61-4.140.20061350.16052618X-RAY DIFFRACTION99.96
4.14-5.210.18291470.15772635X-RAY DIFFRACTION99.75
5.21-57.790.20631340.19232714X-RAY DIFFRACTION99.62
Refinement TLS params.Method: refined / Origin x: -14.261072506 Å / Origin y: 14.8596580542 Å / Origin z: 19.7819984477 Å
111213212223313233
T0.238992104012 Å2-0.0193189823633 Å2-0.00204261153743 Å2-0.223164788283 Å2-0.0441558013383 Å2--0.22550188546 Å2
L0.653053906246 °2-0.213946263538 °20.0259612068177 °2-0.438756039241 °2-0.239386808765 °2--0.499943183369 °2
S-0.00891846250078 Å °-0.0930148026739 Å °0.0870427921351 Å °0.0205063621903 Å °-0.0609227773524 Å °-0.0817519634785 Å °-0.0420647433639 Å °0.0750576186537 Å °0.0585506493633 Å °
Refinement TLS groupSelection details: all

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