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Crystal structure of human Sirt3 in complex with Fluor-de-Lys peptide and piceatannol
Biology and Chemistry Report
4HD8
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE/HYDROLASE INHIBITOR
    Text NAD-dependent deacetylase, Sirtuin, mitochondrial, inhibitor complex, piceatannol, resveratrol-like compound, HYDROLASE-HYDROLASE INHIBITOR complex

    Polymeric Molecules

    Chain A
    Description NAD-dependent protein deacetylase sirtuin-3, mitochondrial 
    Fragment UNP residues 116-399 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 31484.4 
    Source Method genetically manipulated  
    Entity Name hSIRT3, Regulatory protein SIR2 homolog 3, SIR2-like protein 3 
    Chain F
    Description Fluor-de-Lys peptide 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 769.9 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    IPA  ISOPROPYL ALCOHOL  C3 H8 O   60.10  View 
    PIT  PICEATANNOL  C14 H12 O4   244.24  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A SIR3_HUMAN B7Z5U6     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    3.5.1      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    6476   Protein Deacetylation  The Removal of an Acetyl Group From a Protein Amino Acid. an Acetyl Group Is Ch3co Derived From Acetic [ethanoic] Acid. 
    8270   Zinc Ion Binding  Interacting Selectively and Non Covalently with Zinc (zn) Ions. 
    16811   Hydrolase Activity Acting On Carbon Nitrogen (but Not Peptide) Bonds in Linear Amides  Catalysis of the Hydrolysis of Any Non Peptide Carbon Nitrogen Bond in a Linear Amide. 
    51287   NAD Binding  Interacting Selectively and Non Covalently with Nicotinamide Adenine Dinucleotide a Coenzyme Involved in Many Redox and Biosynthetic Reactions; Binding May Be to Either the Oxidized Form Nad+ or the Reduced Form Nadh. 
    70403   Nad+ Binding  Interacting Selectively and Non Covalently with the Oxidized Form NAD of Nicotinamide Adenine Dinucleotide a Coenzyme Involved in Many Redox and Biosynthetic Reactions. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene sir2l3, sirt3
    Host Scientific Name Escherichia coli  
    Host Strain Bl21 (de3) Rosetta2
    Host Vector Type Plasmid
    Host Plasmid Name pVFT3S


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    11 11p15.5 23410     sirtuin 3 SIRT3    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs149834775 LS-SNP   dbSNP   A 133 R - > Q Helix 59% (Exposed) 11 233418
    rs202072152 LS-SNP   dbSNP   A 133 R - > W Helix 59% (Exposed) 11 233419
    rs199655982 LS-SNP   dbSNP   A 143 M - > I Beta Ladder 1% (Buried) 11 233387
    rs144309821 LS-SNP   dbSNP   A 146 A - > V 3/10 Helix 28% (Intermediate) 11 233379
    rs147810576 LS-SNP   dbSNP   A 146 A - > S 3/10 Helix 28% (Intermediate) 11 233380
    rs140359001 LS-SNP   dbSNP   A 151 P - > R 3/10 Helix 43% (Exposed) 11 233364
    rs200996811 LS-SNP   dbSNP   A 174 P - > L Bend 61% (Exposed) 11 233168
    rs199531458 LS-SNP   dbSNP   A 190 K - > R Helix 54% (Exposed) 11 233120
    rs201276555 LS-SNP   dbSNP   A 191 P - > A Helix 2% (Buried) 11 233118
    rs200782697 LS-SNP   dbSNP   A 191 P - > L Helix 2% (Buried) 11 233117
    rs145984757 LS-SNP   dbSNP   A 204 Y - > H Coil 26% (Intermediate) 11 233079
    rs191104319 LS-SNP   dbSNP   A 207 N - > S Coil 15% (Intermediate) 11 233069
    rs11246020 LS-SNP   dbSNP   A 208 V - > FI Helix 21% (Intermediate) 11 233067
    rs200303594 LS-SNP   dbSNP   A 213 L - > I Helix 0% (Buried) 11 233052
    rs1734492 LS-SNP   dbSNP   A 214 R - > GW Helix 13% (Intermediate) 11 233049
    rs200084876 LS-SNP   dbSNP   A 222 L - > P Beta Ladder 4% (Buried) 11 233024
    rs202208408 LS-SNP   dbSNP   A 224 R - > W Beta Ladder 16% (Intermediate) 11 233019
    rs201012829 LS-SNP   dbSNP   A 227 T - > A Beta Ladder 0% (Buried) 11 233010
    rs200625315 LS-SNP   dbSNP   A 235 R - > K Helix 31% (Intermediate) 11 232985
    rs202147171 LS-SNP   dbSNP   A 244 L - > V Beta Ladder 2% (Buried) 11 230529
    rs201248423 LS-SNP   dbSNP   A 248 H - > Y Turn 9% (Intermediate) 11 230517
    rs200275187 LS-SNP   dbSNP   A 250 T - > I Beta Ladder 13% (Intermediate) 11 230510
    rs1734491 LS-SNP   dbSNP   A 255 T - > N Beta Ladder 24% (Intermediate) 11 230495
    rs201985813 LS-SNP   dbSNP   A 261 R - > T Coil 45% (Exposed) 11 230477 ZN
    rs61748606 LS-SNP   dbSNP   A 262 P - > H Beta Ladder 76% (Exposed) 11 230474
    rs199663456 LS-SNP   dbSNP   A 269 R - > Q Helix 42% (Exposed) 11 230453
    rs143392832 LS-SNP   dbSNP   A 276 R - > S Coil 54% (Exposed) 11 224219
    rs199552510 LS-SNP   dbSNP   A 279 R - > G Beta 58% (Exposed) 11 224212
    rs142592164 LS-SNP   dbSNP   A 279 R - > H Beta 58% (Exposed) 11 224211
    rs201576457 LS-SNP   dbSNP   A 281 P - > L Turn 79% (Exposed) 11 224205
    rs147722093 LS-SNP   dbSNP   A 285 G - > S Coil 7% (Buried) 11 224194 ZN
    rs200209873 LS-SNP   dbSNP   A 289 P - > HL Beta Ladder 0% (Buried) 11 224181
    rs201289946 LS-SNP   dbSNP   A 290 D - > N Beta Ladder 28% (Intermediate) 11 224179
    rs145518170 LS-SNP   dbSNP   A 291 I - > V Beta Ladder 0% (Buried) 11 224176
    rs201905714 LS-SNP   dbSNP   A 297 P - > L Beta 63% (Exposed) 11 224157
    rs201762879 LS-SNP   dbSNP   A 306 V - > L Helix 65% (Exposed) 11 224131
    rs200605181 LS-SNP   dbSNP   A 316 L - > F Beta Ladder 2% (Buried) 11 224101
    rs551570 LS-SNP   dbSNP   A 320 T - > N Coil 13% (Intermediate) 11 224088
    rs147582800 LS-SNP   dbSNP   A 334 V - > LM Bend 4% (Buried) 11 219011
    rs202066094 LS-SNP   dbSNP   A 335 R - > W Coil 50% (Exposed) 11 219008
    rs200944124 LS-SNP   dbSNP   A 338 V - > L Bend 2% (Buried) 11 218999
    rs201115579 LS-SNP   dbSNP   A 345 R - > W Bend 60% (Exposed) 11 218978
    rs185287384 LS-SNP   dbSNP   A 346 D - > N Bend 55% (Exposed) 11 218975
    rs149887273 LS-SNP   dbSNP   A 357 S - > R Turn 76% (Exposed) 11 218942
    rs139026266 LS-SNP   dbSNP   A 361 A - > T Beta Ladder 42% (Exposed) 11 218930
    rs200574796 LS-SNP   dbSNP   A 367 V - > I Helix 18% (Intermediate) 11 218912
    rs3020901 LS-SNP   dbSNP   A 369 G - > S Helix 1% (Buried) 11 218906
    rs146003473 LS-SNP   dbSNP   A 370 V - > M Helix 0% (Buried) 11 218903
    rs181924090 LS-SNP   dbSNP   A 379 W - > C Coil 8% (Buried) 11 218874
    rs200928165 LS-SNP   dbSNP   A 380 T - > I Helix 36% (Intermediate) 11 218872
    rs201069150 LS-SNP   dbSNP   A 384 R - > W Helix 63% (Exposed) 11 218861
    rs200076829 LS-SNP   dbSNP   A 386 L - > V Helix 1% (Buried) 11 218855
    rs111450242 LS-SNP   dbSNP   A 388 Q - > R Helix 53% (Exposed) 11 218848
    rs200203977 LS-SNP   dbSNP   A 389 R - > Q Helix 64% (Exposed) 11 218845
    rs139644721 LS-SNP   dbSNP   A 393 K - > N Coil 93% (Exposed) 11 218832