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- PDB-8zvp: Human SIRT6 in complex with EGCG -

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Basic information

Entry
Database: PDB / ID: 8zvp
TitleHuman SIRT6 in complex with EGCG
ComponentsNAD-dependent protein deacylase sirtuin-6
KeywordsHYDROLASE / complex inhibitor Sirtuin
Function / homology
Function and homology information


histone H3K56 deacetylase activity, NAD-dependent / ketone biosynthetic process / histone H3K18 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, hydrolytic mechanism / histone H3K9 deacetylase activity, NAD-dependent / protein delipidation / NAD+-protein-lysine ADP-ribosyltransferase activity / regulation of lipid catabolic process / chromosome, subtelomeric region / positive regulation of protein localization to chromatin ...histone H3K56 deacetylase activity, NAD-dependent / ketone biosynthetic process / histone H3K18 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, hydrolytic mechanism / histone H3K9 deacetylase activity, NAD-dependent / protein delipidation / NAD+-protein-lysine ADP-ribosyltransferase activity / regulation of lipid catabolic process / chromosome, subtelomeric region / positive regulation of protein localization to chromatin / NAD+-protein-arginine ADP-ribosyltransferase activity / pericentric heterochromatin formation / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / positive regulation of stem cell differentiation / DNA damage sensor activity / negative regulation of D-glucose import across plasma membrane / positive regulation of chondrocyte proliferation / cardiac muscle cell differentiation / transposable element silencing / protein acetyllysine N-acetyltransferase / NAD-dependent protein lysine deacetylase activity / histone deacetylase activity, NAD-dependent / positive regulation of blood vessel branching / negative regulation of protein import into nucleus / positive regulation of stem cell proliferation / protein localization to site of double-strand break / protein deacetylation / positive regulation of vascular endothelial cell proliferation / negative regulation of cellular senescence / negative regulation of glycolytic process / TORC2 complex binding / regulation of protein secretion / regulation of double-strand break repair via homologous recombination / negative regulation of gene expression, epigenetic / negative regulation of transcription elongation by RNA polymerase II / positive regulation of stem cell population maintenance / NAD+-protein mono-ADP-ribosyltransferase activity / lncRNA binding / positive regulation of double-strand break repair / response to UV / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of telomere maintenance / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / DNA repair-dependent chromatin remodeling / regulation of lipid metabolic process / subtelomeric heterochromatin formation / negative regulation of gluconeogenesis / determination of adult lifespan / positive regulation of fat cell differentiation / pericentric heterochromatin / regulation of protein localization to plasma membrane / nucleosome binding / positive regulation of protein export from nucleus / nucleotidyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of fibroblast proliferation / protein import into nucleus / negative regulation of protein localization to chromatin / site of DNA damage / circadian regulation of gene expression / positive regulation of insulin secretion / protein destabilization / chromatin DNA binding / base-excision repair / regulation of circadian rhythm / Pre-NOTCH Transcription and Translation / glucose homeostasis / double-strand break repair / transcription corepressor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / positive regulation of cold-induced thermogenesis / Processing of DNA double-strand break ends / damaged DNA binding / chromatin remodeling / negative regulation of cell population proliferation / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein homodimerization activity / DNA binding / nucleoplasm / zinc ion binding / 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 / Chem-KDH / NAD-dependent protein deacylase sirtuin-6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSong, B. / Wang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22277115 China
CitationJournal: To Be Published
Title: SIRT6 in complex with EGCG
Authors: Song, B. / Wang, Y.
History
DepositionJun 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent protein deacylase sirtuin-6
B: NAD-dependent protein deacylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4007
Polymers66,6932
Non-polymers1,7085
Water00
1
A: NAD-dependent protein deacylase sirtuin-6
B: NAD-dependent protein deacylase sirtuin-6
hetero molecules

A: NAD-dependent protein deacylase sirtuin-6
B: NAD-dependent protein deacylase sirtuin-6
hetero molecules

A: NAD-dependent protein deacylase sirtuin-6
B: NAD-dependent protein deacylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,20121
Polymers200,0786
Non-polymers5,12315
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area15670 Å2
ΔGint-60 kcal/mol
Surface area68970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.200, 91.200, 143.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein NAD-dependent protein deacylase sirtuin-6 / NAD-dependent protein deacetylase sirtuin-6 / Protein mono-ADP-ribosyltransferase sirtuin-6 / ...NAD-dependent protein deacetylase sirtuin-6 / Protein mono-ADP-ribosyltransferase sirtuin-6 / Regulatory protein SIR2 homolog 6 / hSIRT6 / SIR2-like protein 6


Mass: 33346.301 Da / Num. of mol.: 2
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, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, protein acetyllysine N-acetyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#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.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-KDH / (2R,3R)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate / (-)-Epigallocatechin-3-gallate / EGCG


Mass: 458.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18O11 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
PH range: 5.3-5.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→45.6 Å / Num. obs: 26481 / % possible obs: 100 % / Redundancy: 19.9 % / Rmerge(I) obs: 0.164 / Net I/σ(I): 13.9
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 1.124 / Num. unique obs: 2747

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.6 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.118 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20524 1141 4.9 %RANDOM
Rwork0.14756 ---
obs0.15029 22302 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 mean: 53.908 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.5→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4387 0 107 0 4494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134597
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174377
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.6586253
X-RAY DIFFRACTIONr_angle_other_deg1.2961.58110095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.095557
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39919.919247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98615772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1721550
X-RAY DIFFRACTIONr_chiral_restr0.080.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025048
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021026
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_it4.7175.3682240
X-RAY DIFFRACTIONr_mcbond_other4.7185.3662239
X-RAY DIFFRACTIONr_mcangle_it6.4238.0462793
X-RAY DIFFRACTIONr_mcangle_other6.4228.0492794
X-RAY DIFFRACTIONr_scbond_it5.1416.0652357
X-RAY DIFFRACTIONr_scbond_other5.1246.0482353
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2368.9033461
X-RAY DIFFRACTIONr_long_range_B_refined10.31517510
X-RAY DIFFRACTIONr_long_range_B_other10.31417511
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.15 74 -
Rwork0.097 1639 -
obs--99.94 %

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