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- PDB-6s2k: Human Menin in complex with AJ21 -

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Basic information

Entry
Database: PDB / ID: 6s2k
TitleHuman Menin in complex with AJ21
ComponentsMultiple endocrine neoplasia I, isoform CRA_b
KeywordsONCOPROTEIN
Function / homology
Function and homology information


negative regulation of cyclin-dependent protein serine/threonine kinase activity / Y-form DNA binding / MLL1/2 complex / osteoblast development / negative regulation of JNK cascade / T-helper 2 cell differentiation / Formation of WDR5-containing histone-modifying complexes / positive regulation of transforming growth factor beta receptor signaling pathway / negative regulation of protein phosphorylation / histone methyltransferase complex ...negative regulation of cyclin-dependent protein serine/threonine kinase activity / Y-form DNA binding / MLL1/2 complex / osteoblast development / negative regulation of JNK cascade / T-helper 2 cell differentiation / Formation of WDR5-containing histone-modifying complexes / positive regulation of transforming growth factor beta receptor signaling pathway / negative regulation of protein phosphorylation / histone methyltransferase complex / negative regulation of cell cycle / R-SMAD binding / cleavage furrow / MLL1 complex / negative regulation of osteoblast differentiation / RHO GTPases activate IQGAPs / negative regulation of DNA-binding transcription factor activity / response to UV / four-way junction DNA binding / transcription repressor complex / transcription initiation-coupled chromatin remodeling / response to gamma radiation / Post-translational protein phosphorylation / Deactivation of the beta-catenin transactivating complex / phosphoprotein binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Formation of the beta-catenin:TCF transactivating complex / nuclear matrix / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / MAPK cascade / double-stranded DNA binding / protein-macromolecule adaptor activity / chromosome, telomeric region / transcription cis-regulatory region binding / endoplasmic reticulum lumen / negative regulation of cell population proliferation / DNA repair / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Chem-KTQ / Menin / Menin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGroves, M.R. / Gao, K.
CitationJournal: To Be Published
Title: Human Menin in complex with AJ21
Authors: Groves, M.R. / Gao, K.
History
DepositionJun 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multiple endocrine neoplasia I, isoform CRA_b
B: Multiple endocrine neoplasia I, isoform CRA_b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6823
Polymers116,2942
Non-polymers3881
Water00
1
A: Multiple endocrine neoplasia I, isoform CRA_b


Theoretical massNumber of molelcules
Total (without water)58,1471
Polymers58,1471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Multiple endocrine neoplasia I, isoform CRA_b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5352
Polymers58,1471
Non-polymers3881
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.399, 101.310, 126.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Multiple endocrine neoplasia I, isoform CRA_b


Mass: 58146.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEN1, hCG_2017452 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A024R5E3, UniProt: O00255*PLUS
#2: Chemical ChemComp-KTQ / ~{N}-[2-(4-methoxyphenyl)ethyl]-2-(4-nitrophenyl)imidazo[1,2-a]pyridin-3-amine


Mass: 388.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20N4O3
Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100mM Bis-Tris propane 200mM KSCN 20% PEG3350 / PH range: 6.7-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0 A
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2019
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→47.04 Å / Num. obs: 19448 / % possible obs: 95.21 % / Redundancy: 3.78 % / CC1/2: 0.97 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.27 / Net I/σ(I): 1.96
Reflection shellResolution: 3.1→3.46 Å / Num. unique obs: 1567 / % possible all: 97.51

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
DIMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→47.04 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.816 / SU B: 28.873 / SU ML: 0.496 / Cross valid method: THROUGHOUT / ESU R Free: 0.603 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29989 947 4.9 %RANDOM
Rwork0.21521 ---
obs0.21936 18465 95.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.123 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2--0.2 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 3.1→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7255 0 29 0 7284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0137454
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176923
X-RAY DIFFRACTIONr_angle_refined_deg1.471.63410131
X-RAY DIFFRACTIONr_angle_other_deg1.1691.5715979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0025923
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48821.935372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.563151199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9431546
X-RAY DIFFRACTIONr_chiral_restr0.0550.2945
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028348
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021611
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8163.3343716
X-RAY DIFFRACTIONr_mcbond_other1.8153.3343715
X-RAY DIFFRACTIONr_mcangle_it3.0914.9964631
X-RAY DIFFRACTIONr_mcangle_other3.0914.9964632
X-RAY DIFFRACTIONr_scbond_it1.6693.4263738
X-RAY DIFFRACTIONr_scbond_other1.673.4283739
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.865.0915501
X-RAY DIFFRACTIONr_long_range_B_refined5.53238.3428393
X-RAY DIFFRACTIONr_long_range_B_other5.53338.3568394
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.098→3.178 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 70 -
Rwork0.313 1341 -
obs--95.08 %

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