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- PDB-6wfg: Crystal structure of human Naa50 in complex with an inhibitor (co... -

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Basic information

Entry
Database: PDB / ID: 6wfg
TitleCrystal structure of human Naa50 in complex with an inhibitor (compound 3) identified using DNA encoded library technology
ComponentsN-alpha-acetyltransferase 50
KeywordsTRANSFERASE/INHIBITOR / N-alpha-acetyltransferase 50 / Inhibitor complex / DNA encoded library / CoA / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


peptidyl-lysine acetyltransferase activity / mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / mitotic sister chromatid cohesion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups ...peptidyl-lysine acetyltransferase activity / mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / mitotic sister chromatid cohesion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / 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-U3V / N-alpha-acetyltransferase 50
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.16 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 1.1Mar 6, 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: N-alpha-acetyltransferase 50
C: N-alpha-acetyltransferase 50
E: N-alpha-acetyltransferase 50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4419
Polymers58,7153
Non-polymers3,7266
Water2,558142
1
A: N-alpha-acetyltransferase 50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8143
Polymers19,5721
Non-polymers1,2422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: N-alpha-acetyltransferase 50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8143
Polymers19,5721
Non-polymers1,2422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: N-alpha-acetyltransferase 50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8143
Polymers19,5721
Non-polymers1,2422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.830, 102.940, 67.640
Angle α, β, γ (deg.)90.000, 106.710, 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 / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-U3V / (2S)-N-[(2S)-3-[1-(3-tert-butyl-1-methyl-1H-pyrazole-5-carbonyl)piperidin-4-yl]-1-(methylamino)-1-oxopropan-2-yl]-6-oxopiperidine-2-carboxamide


Mass: 474.596 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H38N6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 54.72 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Soak of compound into CoA bound 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% ...Details: Soak of compound into CoA bound 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 PILATUS3 S 6M / Detector: PIXEL / Date: Jul 20, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→64.79 Å / Num. obs: 29839 / % possible obs: 88.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 56.42 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.029 / Rrim(I) all: 0.053 / Net I/σ(I): 14.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.16-2.283.30.63928700.7610.4080.7658.1
6.83-64.793.10.02910590.9970.0190.03596.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.31data scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
autoBUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.16→64.79 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.87 / SU R Cruickshank DPI: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.241 / SU Rfree Blow DPI: 0.205 / SU Rfree Cruickshank DPI: 0.209
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1511 5.07 %RANDOM
Rwork0.201 ---
obs0.203 29778 88.5 %-
Displacement parametersBiso max: 138.73 Å2 / Biso mean: 61.08 Å2 / Biso min: 33.88 Å2
Baniso -1Baniso -2Baniso -3
1--15.3445 Å20 Å2-0.1814 Å2
2--10.8871 Å20 Å2
3---4.4574 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 2.16→64.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3676 0 360 142 4178
Biso mean--62.84 64.96 -
Num. residues----453
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1433SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes102HARMONIC2
X-RAY DIFFRACTIONt_gen_planes579HARMONIC5
X-RAY DIFFRACTIONt_it4120HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion503SEMIHARMONIC5
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_contact4582SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4120HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5697HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion17.43
LS refinement shellResolution: 2.16→2.24 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.265 118 4.96 %
Rwork0.235 2259 -
all0.236 2377 -
obs--72.1 %

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