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- PDB-7ak0: Human MALT1(329-729) in complex with a chromane urea containing i... -

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Basic information

Entry
Database: PDB / ID: 7ak0
TitleHuman MALT1(329-729) in complex with a chromane urea containing inhibitor
ComponentsMucosa-associated lymphoid tissue lymphoma translocation protein 1
KeywordsHYDROLASE / Inhibitor / complex / 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 / 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-RJK / Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.316 Å
AuthorsRenatus, M.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of Potent, Highly Selective, and In Vivo Efficacious, Allosteric MALT1 Inhibitors by Iterative Scaffold Morphing.
Authors: Pissot Soldermann, C. / Simic, O. / Renatus, M. / Erbel, P. / Melkko, S. / Wartmann, M. / Bigaud, M. / Weiss, A. / McSheehy, P. / Endres, R. / Santos, P. / Blank, J. / Schuffenhauer, A. / ...Authors: Pissot Soldermann, C. / Simic, O. / Renatus, M. / Erbel, P. / Melkko, S. / Wartmann, M. / Bigaud, M. / Weiss, A. / McSheehy, P. / Endres, R. / Santos, P. / Blank, J. / Schuffenhauer, A. / Bold, G. / Buschmann, N. / Zoller, T. / Altmann, E. / Manley, P.W. / Dix, I. / Buchdunger, E. / Scesa, J. / Quancard, J. / Schlapbach, A. / Bornancin, F. / Radimerski, T. / Regnier, C.H.
History
DepositionSep 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)92,3124
Polymers91,3592
Non-polymers9542
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-0 kcal/mol
Surface area33320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.25, 104.824, 73.284
Angle α, β, γ (deg.)90, 111.14, 90
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: 45679.383 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 (E. coli)
References: UniProt: Q9UDY8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-RJK / 1-[4-[4-(aminomethyl)pyrazol-1-yl]-3-chloranyl-phenyl]-3-[(3~{R})-6-bromanyl-3,4-dihydro-2~{H}-chromen-3-yl]urea


Mass: 476.754 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19BrClN5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5, 0.3 M Magnesium Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.316→68.354 Å / Num. obs: 35677 / % possible obs: 93.3 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.039 / Rrim(I) all: 0.074 / Net I/σ(I): 7.1 / Num. measured all: 122789
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.316-2.3243.70.51415914270.8590.3090.6012.198.2
10.737-68.3543.50.02113843980.9990.0130.02515.998

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Processing

Software
NameVersionClassification
BUSTERrefinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3v55

3v55


Resolution: 2.316→68.35 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.31 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.307 / SU Rfree Blow DPI: 0.211 / SU Rfree Cruickshank DPI: 0.214
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 1814 -RANDOM
Rwork0.1821 ---
obs0.184 35677 93.3 %-
Displacement parametersBiso mean: 51.03 Å2
Baniso -1Baniso -2Baniso -3
1--10.7503 Å20 Å2-0.9529 Å2
2---0.3201 Å20 Å2
3---11.0703 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.316→68.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5701 0 58 268 6027
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085865HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.987926HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2075SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes977HARMONIC5
X-RAY DIFFRACTIONt_it5865HARMONIC10
X-RAY DIFFRACTIONt_nbd10SEMIHARMONIC5
X-RAY DIFFRACTIONt_chiral_improper_torsion743SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4103SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion16.94
LS refinement shellResolution: 2.32→2.33 Å
RfactorNum. reflection% reflection
Rfree0.2975 35 -
Rwork0.1926 --
obs0.1973 714 96.14 %
Refinement TLS params.

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)
11.0662-0.07960.52560.6010.17552.3589-0.0738-0.0692-0.047-0.0692-0.00540.03-0.0470.030.0793-0.0338-0.00460.0184-0.08230.0103-0.06764.45695.697127.0997
20.34270.01140.37261.4583-1.79483.30960.0565-0.18510.2822-0.1851-0.03850.00060.28220.0006-0.018-0.01310.00670.0304-0.09420.0042-0.067913.4141-13.001278.1227
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A337 - 722
2X-RAY DIFFRACTION2{ B|* }B336 - 718

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