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- PDB-6wf5: Crystal structure of human Naa50 in complex with a truncated cofa... -

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Basic information

Entry
Database: PDB / ID: 6wf5
TitleCrystal structure of human Naa50 in complex with a truncated cofactor derived inhibitor (compound 2)
Components
  • ACE-MET-LEU-GLY-PRO-NH2
  • N-alpha-acetyltransferase 50
KeywordsTRANSFERASE/INHIBITOR / N-alpha-acetyltransferase 50 / Inhibitor complex / 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
Chem-U44 / N-alpha-acetyltransferase 50
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.04 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: ACE-MET-LEU-GLY-PRO-NH2
D: ACE-MET-LEU-GLY-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5496
Polymers40,0244
Non-polymers5252
Water1,76598
1
A: N-alpha-acetyltransferase 50
C: ACE-MET-LEU-GLY-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2743
Polymers20,0122
Non-polymers2621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-9 kcal/mol
Surface area9950 Å2
MethodPISA
2
B: N-alpha-acetyltransferase 50
D: ACE-MET-LEU-GLY-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2743
Polymers20,0122
Non-polymers2621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-9 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.937, 52.339, 64.123
Angle α, β, γ (deg.)90.000, 97.380, 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.: 2
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: Protein/peptide ACE-MET-LEU-GLY-PRO-NH2


Mass: 440.581 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-U44 / (2R)-2-hydroxy-3,3-dimethyl-N-{3-oxo-3-[(2-sulfanylethyl)amino]propyl}butanamide


Mass: 262.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H22N2O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 286.15 K / Method: vapor diffusion, sitting drop
Details: Co-crystallization: Naa50 apo protein (14.3 mg/ml) was incubated with compound 2 in a 1:3 molar ratio on ice for 60 min. Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) ...Details: Co-crystallization: Naa50 apo protein (14.3 mg/ml) was incubated with compound 2 in a 1:3 molar ratio on ice for 60 min. Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) PEG 3K/4K was mixed 1:1 with protein:ligand complex

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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: Apr 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: 2.04→63.59 Å / Num. obs: 21247 / % possible obs: 98.8 % / Redundancy: 3.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.126 / Net I/σ(I): 7.9
Reflection shellResolution: 2.04→2.15 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.723 / Num. unique obs: 3080 / CC1/2: 0.667 / % possible all: 98.6

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
autoPROCdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6WF3

6wf3


Resolution: 2.04→50.52 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.846 / SU R Cruickshank DPI: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.237 / SU Rfree Blow DPI: 0.201 / SU Rfree Cruickshank DPI: 0.204
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1023 4.82 %RANDOM
Rwork0.222 ---
obs0.224 21219 98.6 %-
Displacement parametersBiso max: 111.48 Å2 / Biso mean: 35.3 Å2 / Biso min: 10.09 Å2
Baniso -1Baniso -2Baniso -3
1--16.7048 Å20 Å2-6.558 Å2
2--5.5496 Å20 Å2
3---11.1552 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 2.04→50.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 96 98 2815
Biso mean--31.86 35.9 -
Num. residues----324
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d960SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes392HARMONIC5
X-RAY DIFFRACTIONt_it2766HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion345SEMIHARMONIC5
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_contact3152SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2766HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3730HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion19.13
LS refinement shellResolution: 2.04→2.14 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.292 142 5.14 %
Rwork0.245 2619 -
all0.247 2761 -
obs--97.55 %

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