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(-) Description

Title :  SIRT1/ACTIVATOR/SUBSTRATE COMPLEX
 
Authors :  H. Dai
Date :  22 May 15  (Deposition) - 15 Jul 15  (Release) - 23 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.74
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Sirtuin, Activator, Deacylase, Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Dai, A. W. Case, T. V. Riera, T. Considine, J. E. Lee, Y. Hamuro, H. Zhao, Y. Jiang, S. M. Sweitzer, B. Pietrak, B. Schwartz, C. A. Blum, J. S. Disch, R. Caldwell, B. Szczepankiewicz, C. Oalmann, P. Yee Ng, B. H. White, R. Casaubon, R. Narayan, K. Koppetsch, F. Bourbonais, B. Wu, J. Wang, D. Qian, F. Jiang, C. Mao, M. Wang, E. Hu, J. C. Wu, R. B. Perni, G. P. Vlasuk, J. L. Ellis
Crystallographic Structure Of A Small Molecule Sirt1 Activator-Enzyme Complex.
Nat Commun V. 6 7645 2015
PubMed-ID: 26134520  |  Reference-DOI: 10.1038/NCOMMS8645

(-) Compounds

Molecule 1 - NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-1
    Chains: A
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SIRT1, SIR2L1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HSIRT1,REGULATORY PROTEIN SIR2 HOMOLOG 1,SIR2-LIKE PROTEIN 1,HSIR2
 
Molecule 2 - AC-P53
    Chains: B
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 7)

Asymmetric Unit (6, 7)
No.NameCountTypeFull Name
14TQ1Ligand/Ion(3S)-1,3-DIMETHYL-N-[3-(1,3-OXAZOL-5-YL)PHENYL]-6-[3-(TRIFLUOROMETHYL)PHENYL]-2,3-DIHYDROPYRIDO[2,3-B]PYRAZINE-4(1H)-CARBOXAMIDE
2ALY1Mod. Amino AcidN(6)-ACETYLLYSINE
3CNA1Ligand/IonCARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4GOL2Ligand/IonGLYCEROL
5NLE1Mod. Amino AcidNORLEUCINE
6ZN1Ligand/IonZINC ION
Biological Unit 1 (5, 6)
No.NameCountTypeFull Name
14TQ1Ligand/Ion(3S)-1,3-DIMETHYL-N-[3-(1,3-OXAZOL-5-YL)PHENYL]-6-[3-(TRIFLUOROMETHYL)PHENYL]-2,3-DIHYDROPYRIDO[2,3-B]PYRAZINE-4(1H)-CARBOXAMIDE
2ALY1Mod. Amino AcidN(6)-ACETYLLYSINE
3CNA1Ligand/IonCARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4GOL2Ligand/IonGLYCEROL
5NLE1Mod. Amino AcidNORLEUCINE
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (5, 12)
No.NameCountTypeFull Name
14TQ2Ligand/Ion(3S)-1,3-DIMETHYL-N-[3-(1,3-OXAZOL-5-YL)PHENYL]-6-[3-(TRIFLUOROMETHYL)PHENYL]-2,3-DIHYDROPYRIDO[2,3-B]PYRAZINE-4(1H)-CARBOXAMIDE
2ALY2Mod. Amino AcidN(6)-ACETYLLYSINE
3CNA2Ligand/IonCARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4GOL4Ligand/IonGLYCEROL
5NLE2Mod. Amino AcidNORLEUCINE
6ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:371 , CYS A:374 , CYS A:395 , CYS A:398binding site for residue ZN A 701
2AC2SOFTWAREGLY A:261 , ALA A:262 , GLY A:263 , VAL A:266 , ILE A:270 , PRO A:271 , ASP A:272 , PHE A:273 , ARG A:274 , PHE A:297 , ILE A:316 , GLN A:345 , ASN A:346 , ILE A:347 , ASP A:348 , GLY A:440 , SER A:441 , SER A:442 , ASN A:465 , ARG A:466 , GLU A:467 , GLY A:480 , ASP A:481 , CYS A:482 , HOH A:809 , HOH A:813 , ALY B:4binding site for residue CNA A 702
3AC3SOFTWARELEU A:206 , THR A:209 , PRO A:211 , PRO A:212 , GLN A:222 , ILE A:223 , ASN A:226 , ILE A:227 , GLU A:230binding site for residue 4TQ A 703
4AC4SOFTWAREVAL A:353 , ALA A:382 , VAL A:383 , ASP A:386 , PRO A:396binding site for residue GOL A 704
5AC5SOFTWAREPHE A:422 , HIS A:423 , LEU A:450 , SER A:454binding site for residue GOL A 705

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZZJ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:446 -Pro A:447
2Pro A:646 -Pro A:647

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZZJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZZJ)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZZJ)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:344
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...hhhhhhhhhh.........hhhhhhhhhhhhhh............hhhhhhhhhhhh..eeeee.hhhhhhhh.........hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhhh...eee..eeeeeeee.....eeehhhhhhhhhh.................eeeee.......hhhhhhhhhhhh....eeeee.....eehhhhhhhhh.....eeeee..........eeee.hhhhhhhhhhhhhhhhhhh.........eee...eee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zzj A 183 GPYTFVQQHLMIGTDPRTILKDLLPETIPPPELDDMTLWQIVINILSEPPKRKKRKDINTIEDAVKLLQECKKIIVLTGAGVSVSCGIPDFRSRDGIYARLAVDFPDLPDPQAMFDIEYFRKDPRPFFKFAKEIYPGQFQPSLCHKFIALSDKEGKLLRNYTQNIDTLEQVAGIQRIIQCHGSFATASCLICKYKVDCEAVRGDIFNQVVPRCPRCPADEPLAIMKPEIVFFGENLPEQFHRAMKYDKDEVDLLIVIGSSLKVRPVALIPSSIPHEVPQILINREPLPHLHFDVELLGDCDVIINELCHRLGGEYAKLCCNGGSQYLFLPPNRYIFHGAEVYSD 660
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502||     646       656    
                                                                                                                                                                                                                                                                                                                                                          503|                      
                                                                                                                                                                                                                                                                                                                                                           638                      


Chain B from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....ee. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 4zzj B   1 RHKxLxF   7
                               | | 
                               4-ALY
                                 6-NLE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4ZZJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZZJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZZJ)

(-) Gene Ontology  (249, 283)

Asymmetric Unit(hide GO term definitions)

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  SIR1_HUMAN | Q96EB6
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  3.5.1.-
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        P53_HUMAN | P04637: 1a1u 1aie 1c26 1dt7 1gzh 1h26 1hs5 1jsp 1kzy 1ma3 1olg 1olh 1pes 1pet 1sae 1saf 1sak 1sal 1tsr 1tup 1uol 1xqh 1yc5 1ycq 1ycr 1ycs 2ac0 2ady 2ahi 2ata 2b3g 2bim 2bin 2bio 2bip 2biq 2f1x 2fej 2foj 2foo 2gs0 2h1l 2h2d 2h2f 2h4f 2h4h 2h4j 2h59 2j0z 2j10 2j11 2j1w 2j1x 2j1y 2j1z 2j20 2j21 2k8f 2l14 2ly4 2mej 2mwo 2mwp 2mwy 2mzd 2ocj 2pcx 2ruk 2vuk 2wgx 2x0u 2x0v 2x0w 2xwr 2ybg 2ydr 2z5s 2z5t 3d05 3d06 3d07 3d08 3d09 3d0a 3dab 3dac 3igk 3igl 3kmd 3kz8 3lw1 3oq5 3pdh 3q01 3q05 3q06 3sak 3tg5 3ts8 3zme 4agl 4agm 4agn 4ago 4agp 4agq 4buz 4bv2 4fz3 4hfz 4hje 4ibq 4ibs 4ibt 4ibu 4ibv 4ibw 4iby 4ibz 4ijt 4kvp 4lo9 4loe 4lof 4mzi 4mzr 4qo1 4rp6 4rp7 4x34 4xr8 5a7b 5ab9 5aba 5aoi 5aoj 5aok 5aol 5aom 5bua 5ecg 5g4m 5g4n 5g4o 5hou 5hp0 5hpd 5lap 5lgy 5un8
        SIR1_HUMAN | Q96EB6: 4i5i 4if6 4ig9 4kxq 4zzh 4zzi 5btr

(-) Related Entries Specified in the PDB File

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