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- PDB-4c7b: Complex of human Sirt3 with Bromo-Resveratrol and Fluor-De-Lys peptide -

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Basic information

Entry
Database: PDB / ID: 4c7b
TitleComplex of human Sirt3 with Bromo-Resveratrol and Fluor-De-Lys peptide
Components
  • NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
  • PEPTIDE
KeywordsHYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX / HYDROLASE / SIRTUIN / INHIBITOR / ACTIVATION / RESVERATROL / SIRT1 / METABOLIC SENSOR / METABOLISM / AGING
Function / homology
Function and homology information


positive regulation of superoxide dismutase activity / positive regulation of catalase activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / Maturation of TCA enzymes and regulation of TCA cycle / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / protein deacetylation / histone deacetylase activity, NAD-dependent ...positive regulation of superoxide dismutase activity / positive regulation of catalase activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / Maturation of TCA enzymes and regulation of TCA cycle / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / protein deacetylation / histone deacetylase activity, NAD-dependent / positive regulation of oxidative phosphorylation / Regulation of FOXO transcriptional activity by acetylation / protein lysine deacetylase activity / cellular response to stress / negative regulation of reactive oxygen species metabolic process / NAD+ binding / Mitochondrial unfolded protein response (UPRmt) / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / aerobic respiration / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / negative regulation of ERK1 and ERK2 cascade / sequence-specific DNA binding / mitochondrial matrix / enzyme binding / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily ...SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-[(E)-2-(4-bromophenyl)ethenyl]benzene-1,3-diol / ISOPROPYL ALCOHOL / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNguyen, G.T.T. / Gertz, M. / Weyand, M. / Steegborn, C.
CitationJournal: Chem.Biol. / Year: 2013
Title: Crystal Structures of Sirt3 Complexes with 4'-Bromo-Resveratrol Reveal Binding Sites and Inhibition Mechanism.
Authors: Nguyen, G.T.T. / Gertz, M. / Steegborn, C.
History
DepositionSep 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3Dec 14, 2016Group: Source and taxonomy
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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-3, MITOCHONDRIAL
B: PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8908
Polymers32,1972
Non-polymers6936
Water2,450136
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-5.9 kcal/mol
Surface area12700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.820, 114.820, 123.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1396-

IPA

21A-2041-

HOH

31A-2064-

HOH

41A-2083-

HOH

51A-2094-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL


Mass: 31427.162 Da / Num. of mol.: 1 / Fragment: RESIDUES 117-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PVFT3S / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide PEPTIDE


Mass: 769.913 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 5 types, 142 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-BVB / 5-[(E)-2-(4-bromophenyl)ethenyl]benzene-1,3-diol


Mass: 291.140 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11BrO2
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7
Details: 200 MM NACL,100 MM HEPES PH 7, 10% (V/V) ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.92039
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 29, 2011 / Details: COLLIMATOR
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92039 Å / Relative weight: 1
ReflectionResolution: 2.1→46.1 Å / Num. obs: 35487 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4H8D

4h8d
PDB Unreleased entry


Resolution: 2.1→46.13 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.863 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23402 925 5 %RANDOM
Rwork0.18046 ---
obs0.18305 17585 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: 39.286 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å2-0.35 Å20 Å2
2---0.71 Å20 Å2
3---2.29 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2113 0 40 136 2289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192209
X-RAY DIFFRACTIONr_bond_other_d0.0030.022158
X-RAY DIFFRACTIONr_angle_refined_deg2.1182.0083000
X-RAY DIFFRACTIONr_angle_other_deg1.0693.0044954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6745264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82722.52695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64615353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0291520
X-RAY DIFFRACTIONr_chiral_restr0.1130.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212430
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02505
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_it1.7151.3871059
X-RAY DIFFRACTIONr_mcbond_other1.7151.3891060
X-RAY DIFFRACTIONr_mcangle_it2.812.0551319
X-RAY DIFFRACTIONr_mcangle_other2.8092.0571320
X-RAY DIFFRACTIONr_scbond_it2.3821.8781149
X-RAY DIFFRACTIONr_scbond_other2.3811.8781150
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5882.6771681
X-RAY DIFFRACTIONr_long_range_B_refined9.01513.9442564
X-RAY DIFFRACTIONr_long_range_B_other9.01413.9492565
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 67 -
Rwork0.286 1283 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -33.98 Å / Origin y: -16.737 Å / Origin z: 7.823 Å
111213212223313233
T0.3274 Å2-0.0612 Å20.0398 Å2-0.3378 Å2-0.0041 Å2--0.0226 Å2
L1.3064 °2-0.666 °20.1619 °2-0.9771 °20.2056 °2--0.8636 °2
S-0.0168 Å °-0.0087 Å °0.1028 Å °-0.1188 Å °0.065 Å °-0.1394 Å °-0.1302 Å °0.1223 Å °-0.0482 Å °

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