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- PDB-6wfk: Crystal structure of human Naa50 in complex with CoA and an inhib... -

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Basic information

Entry
Database: PDB / ID: 6wfk
TitleCrystal structure of human Naa50 in complex with CoA and an inhibitor (compound 4a) identified using DNA encoded library technology
ComponentsN-alpha-acetyltransferase 50
KeywordsTRANSFERASE / N-alpha-acetyltransferase 50 / Inhibitor complex / DNA encoded library / CoA
Function / homology
Function and homology information


mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal protein amino acid acetylation / NatA complex / protein N-terminal-methionine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / mitotic sister chromatid cohesion / protein-lysine-acetyltransferase activity ...mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal protein amino acid acetylation / NatA complex / protein N-terminal-methionine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / mitotic sister chromatid cohesion / protein-lysine-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / post-translational protein modification / nucleolus / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Chem-U2J / N-alpha-acetyltransferase 50
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.87 Å
AuthorsGreasley, S.E. / Feng, J. / Deng, Y.-L. / Stewart, A.E.
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: Characterization of SpecificN-alpha-Acetyltransferase 50 (Naa50) Inhibitors Identified Using a DNA Encoded Library.
Authors: Kung, P.P. / Bingham, P. / Burke, B.J. / Chen, Q. / Cheng, X. / Deng, Y.L. / Dou, D. / Feng, J. / Gallego, G.M. / Gehring, M.R. / Grant, S.K. / Greasley, S. / Harris, A.R. / Maegley, K.A. / ...Authors: Kung, P.P. / Bingham, P. / Burke, B.J. / Chen, Q. / Cheng, X. / Deng, Y.L. / Dou, D. / Feng, J. / Gallego, G.M. / Gehring, M.R. / Grant, S.K. / Greasley, S. / Harris, A.R. / Maegley, K.A. / Meier, J. / Meng, X. / Montano, J.L. / Morgan, B.A. / Naughton, B.S. / Palde, P.B. / Paul, T.A. / Richardson, P. / Sakata, S. / Shaginian, A. / Sonnenburg, W.K. / Subramanyam, C. / Timofeevski, S. / Wan, J. / Yan, W. / Stewart, A.E.
History
DepositionApr 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-alpha-acetyltransferase 50
B: N-alpha-acetyltransferase 50
C: N-alpha-acetyltransferase 50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6759
Polymers58,7153
Non-polymers3,9606
Water4,702261
1
A: N-alpha-acetyltransferase 50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8923
Polymers19,5721
Non-polymers1,3202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-alpha-acetyltransferase 50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8923
Polymers19,5721
Non-polymers1,3202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-alpha-acetyltransferase 50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8923
Polymers19,5721
Non-polymers1,3202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.350, 102.380, 67.550
Angle α, β, γ (deg.)90.000, 106.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein N-alpha-acetyltransferase 50 / hNaa50p / N-acetyltransferase 13 / N-acetyltransferase 5 / hNAT5 / N-acetyltransferase san homolog ...hNaa50p / N-acetyltransferase 13 / N-acetyltransferase 5 / hNAT5 / N-acetyltransferase san homolog / hSAN / N-epsilon-acetyltransferase 50 / NatE catalytic subunit / Naa50


Mass: 19571.502 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA50, MAK3, NAT13, NAT5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9GZZ1, N-terminal methionine Nalpha-acetyltransferase NatE, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-U2J / (4S)-1-methyl-N-{(3S,5S)-5-[4-(methylcarbamoyl)-1,3-thiazol-2-yl]-1-[4-(1H-tetrazol-5-yl)benzene-1-carbonyl]pyrrolidin-3-yl}-2,6-dioxohexahydropyrimidine-4-carboxamide


Mass: 552.566 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H24N10O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Compound 4a soaked into crystals of Naa50+CoA. CoA co-crystals: Naa50 apo protein (14.3 mg/ml) was incubated with CoA in a 1:3 molar ratio on ice for 60 min. Crystallization solution: 0.1 M ...Details: Compound 4a soaked into crystals of Naa50+CoA. CoA co-crystals: Naa50 apo protein (14.3 mg/ml) was incubated with CoA in a 1:3 molar ratio on ice for 60 min. Crystallization solution: 0.1 M Na acetate, pH5.0, 25% (w/v) PEG 3350, 10 mM Dithiothreitol (DTT), and 0.1% Dioxane

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→64.63 Å / Num. obs: 38205 / % possible obs: 91.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 43.19 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.9
Reflection shellResolution: 1.87→2.03 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1910 / CC1/2: 0.421 / % possible all: 55.5

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Processing

Software
NameVersionClassification
XDSdata reduction
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
autoPROCdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: unpublished model, solved using PDB entry 2Ob0

2ob0


Resolution: 1.87→64.63 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.944 / SU R Cruickshank DPI: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.185 / SU Rfree Blow DPI: 0.152 / SU Rfree Cruickshank DPI: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1853 4.85 %RANDOM
Rwork0.2 ---
obs0.201 38205 73.5 %-
Displacement parametersBiso max: 119.49 Å2 / Biso mean: 47.48 Å2 / Biso min: 25.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.5176 Å20 Å20.0201 Å2
2--0.4929 Å20 Å2
3---0.0247 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 1.87→64.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3698 0 330 261 4289
Biso mean--49.81 55.25 -
Num. residues----456
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1441SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes717HARMONIC5
X-RAY DIFFRACTIONt_it4118HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion508SEMIHARMONIC5
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_contact4750SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4118HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5649HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion17.05
LS refinement shellResolution: 1.87→1.98 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2376 34 4.44 %
Rwork0.219 731 -

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