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- PDB-7cl0: Crystal structure of human SIRT6 -

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Basic information

Entry
Database: PDB / ID: 7cl0
TitleCrystal structure of human SIRT6
Components
  • NAD-dependent protein deacetylase sirtuin-6
  • THR-ALA-ARG-LYS-SER-THR-GLY
KeywordsTRANSFERASE / deacylase
Function / homology
Function and homology information


NAD-dependent histone H3K56 deacetylase activity / NAD-dependent histone H3K18 deacetylase activity / NAD-dependent histone H3K9 deacetylase activity / protein delipidation / ketone biosynthetic process / regulation of lipid catabolic process / NAD+-protein-lysine ADP-ribosyltransferase activity / chromosome, subtelomeric region / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity ...NAD-dependent histone H3K56 deacetylase activity / NAD-dependent histone H3K18 deacetylase activity / NAD-dependent histone H3K9 deacetylase activity / protein delipidation / ketone biosynthetic process / regulation of lipid catabolic process / NAD+-protein-lysine ADP-ribosyltransferase activity / chromosome, subtelomeric region / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / positive regulation of protein localization to chromatin / DNA damage sensor activity / positive regulation of stem cell differentiation / positive regulation of blood vessel branching / NAD-dependent protein lysine deacetylase activity / retrotransposon silencing / protein acetyllysine N-acetyltransferase / cardiac muscle cell differentiation / positive regulation of chondrocyte proliferation / pericentric heterochromatin formation / positive regulation of telomere maintenance / protein deacetylation / negative regulation of glucose import / protein localization to site of double-strand break / NAD-dependent histone deacetylase activity / TORC2 complex binding / lncRNA binding / negative regulation of glycolytic process / negative regulation of protein localization to chromatin / positive regulation of double-strand break repair / DNA repair-dependent chromatin remodeling / positive regulation of vascular endothelial cell proliferation / negative regulation of protein import into nucleus / negative regulation of gene expression, epigenetic / regulation of double-strand break repair via homologous recombination / positive regulation of stem cell population maintenance / positive regulation of stem cell proliferation / regulation of protein secretion / negative regulation of transcription elongation by RNA polymerase II / NAD+-protein ADP-ribosyltransferase activity / negative regulation of cellular senescence / site of DNA damage / regulation of lipid metabolic process / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / NAD+ binding / subtelomeric heterochromatin formation / positive regulation of fat cell differentiation / regulation of protein localization to plasma membrane / pericentric heterochromatin / negative regulation of gluconeogenesis / response to UV / nucleosome binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / nucleotidyltransferase activity / positive regulation of protein export from nucleus / determination of adult lifespan / circadian regulation of gene expression / protein destabilization / base-excision repair / regulation of circadian rhythm / positive regulation of insulin secretion / chromatin DNA binding / Pre-NOTCH Transcription and Translation / transcription corepressor activity / positive regulation of fibroblast proliferation / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / glucose homeostasis / positive regulation of cold-induced thermogenesis / site of double-strand break / Processing of DNA double-strand break ends / damaged DNA binding / chromatin remodeling / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein homodimerization activity / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
Chem-AR6 / tetradecanethial / DI(HYDROXYETHYL)ETHER / NAD-dependent protein deacylase sirtuin-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsSong, K. / Zhang, J.
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Reply to: Binding site for MDL-801 on SIRT6.
Authors: Huang, Z. / Zhao, J. / Deng, W. / Chen, Y. / Shang, J. / Song, K. / Zhang, L. / Wang, C. / Lu, S. / Yang, X. / He, B. / Min, J. / Hu, H. / Tan, M. / Xu, J. / Zhang, Q. / Zhong, J. / Sun, X. ...Authors: Huang, Z. / Zhao, J. / Deng, W. / Chen, Y. / Shang, J. / Song, K. / Zhang, L. / Wang, C. / Lu, S. / Yang, X. / He, B. / Min, J. / Hu, H. / Tan, M. / Xu, J. / Zhang, Q. / Zhong, J. / Sun, X. / Mao, Z. / Lin, H. / Xiao, M. / Chin, Y.E. / Jiang, H. / Shen, H. / Xu, Y. / Chen, G. / Zhang, J.
History
DepositionJul 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 12, 2021Group: 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 1.3Nov 29, 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
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: NAD-dependent protein deacetylase sirtuin-6
D: THR-ALA-ARG-LYS-SER-THR-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,31222
Polymers40,0882
Non-polymers2,22420
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-90 kcal/mol
Surface area14310 Å2
Unit cell
Length a, b, c (Å)161.795, 161.795, 161.795
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11D-204-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AD

#1: Protein NAD-dependent protein deacetylase sirtuin-6 / Regulatory protein SIR2 homolog 6 / SIR2-like protein 6


Mass: 39180.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT6, SIR2L6 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8N6T7, protein acetyllysine N-acetyltransferase
#2: Protein/peptide THR-ALA-ARG-LYS-SER-THR-GLY


Mass: 906.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 7 types, 254 molecules

#3: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-G4U / tetradecanethial


Mass: 228.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28S
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.4 Å3/Da / Density % sol: 72.06 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M (NH4)2SO4, 0.1 M Mes pH 6.5, 20% W/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jan 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.53→114.41 Å / Num. obs: 24693 / % possible obs: 100 % / Redundancy: 22.4 % / CC1/2: 0.995 / Net I/σ(I): 24
Reflection shellResolution: 2.53→2.62 Å / Num. unique obs: 2416 / CC1/2: 0.836

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X16

5x16


Resolution: 2.53→114.41 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.868 / SU B: 6.606 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 1251 5.1 %RANDOM
Rwork0.2064 ---
obs0.2085 23434 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 154.33 Å2 / Biso mean: 45.614 Å2 / Biso min: 16.61 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.53→114.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2337 0 131 234 2702
Biso mean--60.6 44.38 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192516
X-RAY DIFFRACTIONr_bond_other_d0.0020.022440
X-RAY DIFFRACTIONr_angle_refined_deg2.0752.0243396
X-RAY DIFFRACTIONr_angle_other_deg1.1243.0015616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0175301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71422.059102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02415414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7981528
X-RAY DIFFRACTIONr_chiral_restr0.1110.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212686
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02539
LS refinement shellResolution: 2.532→2.598 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 95 -
Rwork0.278 1673 -
all-1768 -
obs--100 %

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