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- PDB-4bn5: Structure of human SIRT3 in complex with SRT1720 inhibitor -

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Basic information

Entry
Database: PDB / ID: 4bn5
TitleStructure of human SIRT3 in complex with SRT1720 inhibitor
ComponentsNAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
KeywordsHYDROLASE / LYSINE DEACETYLASE / ADP RIBOSE
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
CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-SR7 / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsNguyen, G.T.T. / Schaefer, S. / Gertz, M. / Weyand, M. / Steegborn, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structures of Human Sirtuin 3 Complexes with Adp-Ribose and with Carba-Nad+ and Srt1720: Binding Details and Inhibition Mechanism
Authors: Nguyen, G.T.T. / Schaefer, S. / Gertz, M. / Weyand, M. / Steegborn, C.
History
DepositionMay 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Dec 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
B: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
C: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
D: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
E: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
F: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
G: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
H: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
I: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
J: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
K: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
L: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)389,77452
Polymers375,03612
Non-polymers14,73840
Water00
1
A: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4504
Polymers31,2531
Non-polymers1,1973
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4504
Polymers31,2531
Non-polymers1,1973
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5435
Polymers31,2531
Non-polymers1,2904
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5435
Polymers31,2531
Non-polymers1,2904
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4504
Polymers31,2531
Non-polymers1,1973
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4504
Polymers31,2531
Non-polymers1,1973
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4504
Polymers31,2531
Non-polymers1,1973
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4504
Polymers31,2531
Non-polymers1,1973
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4504
Polymers31,2531
Non-polymers1,1973
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4504
Polymers31,2531
Non-polymers1,1973
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5435
Polymers31,2531
Non-polymers1,2904
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5435
Polymers31,2531
Non-polymers1,2904
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)227.820, 246.060, 127.340
Angle α, β, γ (deg.)90.00, 123.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL / HSIRT3 / REGULATORY PROTEIN SIR2 HOMOLOG 3 / SIR2-LIKE PROTEIN 3


Mass: 31253.010 Da / Num. of mol.: 12
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: Chemical
ChemComp-CNA / CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 662.460 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C22H30N7O13P2
#3: Chemical
ChemComp-SR7 / N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide


Mass: 469.561 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C25H23N7OS
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
Has protein modificationY

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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: 4.41 Å3/Da / Density % sol: 72.1 % / Description: NONE
Crystal growDetails: 20% (W/V) PEG3350, 0.2 M SODIUM FLUORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2013 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 3.25→25 Å / Num. obs: 91158 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.3
Reflection shellResolution: 3.25→3.3 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.44 / Mean I/σ(I) obs: 1.1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GLS

3gls


Resolution: 3.25→48.57 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.903 / SU B: 55.678 / SU ML: 0.442 / Cross valid method: THROUGHOUT / ESU R: 1.335 / ESU R Free: 0.486 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.26534 4558 5 %RANDOM
Rwork0.20791 ---
obs0.21073 86600 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 97.868 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å2-0.07 Å2
2---3.78 Å20 Å2
3---2.47 Å2
Refinement stepCycle: LAST / Resolution: 3.25→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25548 0 972 0 26520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227353
X-RAY DIFFRACTIONr_bond_other_d0.0040.0226031
X-RAY DIFFRACTIONr_angle_refined_deg2.222.03137404
X-RAY DIFFRACTIONr_angle_other_deg1.1643.01559812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.61553263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6522.8671123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.223154187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.36215217
X-RAY DIFFRACTIONr_chiral_restr0.0870.24200
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02130057
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026166
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.25→3.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 335 -
Rwork0.359 6377 -
obs--99.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.53660.36610.92954.3277-0.85153.5746-0.09910.68990.53640.27050.51220.357-0.4560.4155-0.41310.31960.04210.23790.89680.19840.2608223.47587.774117.3114
24.4836-0.62141.82273.56750.67055.9474-0.2760.5616-0.31480.42870.56220.15270.63420.4575-0.28620.40060.18950.20240.8285-0.04620.2124213.3649-24.783910.5002
32.8013-0.30250.17587.82931.37734.59750.4198-0.19970.30821.4821-0.21670.26080.34390.6654-0.20311.07980.05620.40390.5758-0.00080.1913215.3393-2.536447.9953
43.96550.4475-0.19377.474-0.16853.02840.08390.50310.32880.8816-0.23311.29850.5404-0.34050.14920.62460.0220.640.55690.02660.7466188.368-14.49529.8701
52.62990.098-0.31913.83990.24045.97280.0876-0.17960.07280.12570.0216-0.53930.05380.0499-0.10910.3456-0.00580.07780.4289-0.12250.9281209.3233-55.168654.9704
64.2466-1.0356-1.02793.5350.70093.40670.0239-0.2394-0.40410.6350.2359-0.38550.627-0.1306-0.25970.8057-0.0777-0.4370.56960.08060.679262.9589-24.43332.1907
74.2486-0.0269-1.52493.61940.02013.541-0.0462-0.03770.0842-0.5030.01150.34870.1219-0.0930.03470.8699-0.1348-0.16640.43170.01940.4713183.922138.264837.6098
85.4294-0.33640.93443.95850.34552.4448-0.15140.07070.1889-0.93160.0063-0.1109-0.56990.1490.14511.2124-0.2004-0.26250.45260.12570.5977193.9267.890935.6352
93.5660.24931.53073.8992-0.38874.8116-0.04740.2104-0.6347-0.36380.0576-0.71610.21420.0213-0.01020.49650.04870.04250.4355-0.2061.2198207.4232-84.98344.8877
102.62650.3547-0.22253.5037-1.2134.4134-0.0945-0.22150.6236-0.09180.1730.7479-0.4335-0.0887-0.07850.3840.0486-0.26430.5751-0.09861.097184.79287.4064-20.5768
111.3742-0.15590.11494.8858-0.4791.94810.0427-0.4579-0.12591.51470.0424-0.7844-0.0728-0.2088-0.08511.65930.1157-0.99680.7431-0.10341.3539282.6849-14.07157.2237
122.4623-0.0568-0.10895.7370.2691.8671-0.1440.4346-0.01690.2337-0.0048-1.8464-0.09320.25760.14880.64770.0339-0.61980.7307-0.12672.2598301.2626-2.982229.6758
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A122 - 394
2X-RAY DIFFRACTION2B122 - 394
3X-RAY DIFFRACTION3C122 - 394
4X-RAY DIFFRACTION4D122 - 393
5X-RAY DIFFRACTION5E122 - 394
6X-RAY DIFFRACTION6F122 - 394
7X-RAY DIFFRACTION7G122 - 394
8X-RAY DIFFRACTION8H122 - 394
9X-RAY DIFFRACTION9I122 - 394
10X-RAY DIFFRACTION10J122 - 394
11X-RAY DIFFRACTION11K122 - 394
12X-RAY DIFFRACTION12L122 - 394

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