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- PDB-7x3p: Crystal structure of human SIRT5 in complex with diazirine inhibitor 9 -

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Basic information

Entry
Database: PDB / ID: 7x3p
TitleCrystal structure of human SIRT5 in complex with diazirine inhibitor 9
ComponentsNAD-dependent protein deacylase sirtuin-5, mitochondrial
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor / complex / hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


protein demalonylation / protein deglutarylation / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity ...protein demalonylation / protein deglutarylation / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity / protein deacetylation / histone deacetylase activity, NAD-dependent / negative regulation of cardiac muscle cell apoptotic process / negative regulation of reactive oxygen species metabolic process / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to ischemia / mitochondrion organization / response to nutrient levels / Transcriptional activation of mitochondrial biogenesis / mitochondrial intermembrane space / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / zinc ion binding / nucleus / cytosol
Similarity search - Function
Sirtuin, class III / Sirtuin, catalytic core small domain superfamily / 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-8VG / DI(HYDROXYETHYL)ETHER / NAD-dependent protein deacylase sirtuin-5, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.56 Å
AuthorsLi, G.-B. / Deng, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82122065, 82073698 China
CitationJournal: To Be Published
Title: Crystal structure of human SIRT5 in complex with diazirine inhibitor 9
Authors: Li, G.-B. / Deng, J.
History
DepositionMar 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent protein deacylase sirtuin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0304
Polymers30,1831
Non-polymers8463
Water7,044391
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint4 kcal/mol
Surface area12060 Å2
Unit cell
Length a, b, c (Å)41.332, 65.034, 55.658
Angle α, β, γ (deg.)90.000, 93.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NAD-dependent protein deacylase sirtuin-5, mitochondrial / Regulatory protein SIR2 homolog 5 / SIR2-like protein 5


Mass: 30183.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT5, SIR2L5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9NXA8, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-8VG / 5-[[(5~{S})-6-[[(1~{S})-1-(4-hydroxyphenyl)-2-oxidanylidene-2-(prop-2-ynylamino)ethyl]amino]-6-oxidanylidene-5-[[4-[3-(trifluoromethyl)-1,2-diazirin-3-yl]phenyl]carbonylamino]hexyl]amino]-5-sulfanylidene-pentanoic acid


Type: peptide-like / Mass: 674.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H33F3N6O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 23%-27% (v/v) PEG 3350, 0.1 M MES, pH 5.5-6.0, 0.1-0.2 M NaCl
PH range: 5.5-6.0

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Data collection

DiffractionMean temperature: 198 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Nov 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.56→55.55 Å / Num. obs: 41469 / % possible obs: 96.7052 % / Redundancy: 1.498 % / Biso Wilson estimate: 11.57 Å2 / Rrim(I) all: 0.676 / Net I/σ(I): 0.1
Reflection shellResolution: 1.56→1.656 Å / Rrim(I) all: 0.676

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.18 Å42.24 Å
Translation1.18 Å42.24 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.6.0phasing
PHENIX1.20.1-4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EQS

6eqs


Resolution: 1.56→27.775 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 15.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1634 1187 2.93 %
Rwork0.1388 39366 -
obs0.1395 40553 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.69 Å2 / Biso mean: 15.2122 Å2 / Biso min: 4.1 Å2
Refinement stepCycle: final / Resolution: 1.56→27.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 0 55 393 2489
Biso mean--16.22 28.42 -
Num. residues----267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092212
X-RAY DIFFRACTIONf_angle_d1.133001
X-RAY DIFFRACTIONf_chiral_restr0.062316
X-RAY DIFFRACTIONf_plane_restr0.008398
X-RAY DIFFRACTIONf_dihedral_angle_d20.5091308
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.56-1.6310.181490.137486496
1.631-1.7170.1671530.1365488396
1.6805-1.75690.18021510.1513478893
1.717-1.82450.16691470.1287490397
1.8245-1.96540.15451340.1286494897
1.9654-2.16310.13471550.1294495498
2.1631-2.47590.16071490.129500198
2.4759-3.11870.15581490.1438502598

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