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(-) Description

Title :  HUMAN SIRT6 IN COMPLEX WITH ACTIVATOR UBCS039
 
Authors :  C. Steegborn, W. You, C. Kambach
Date :  17 Nov 16  (Deposition) - 28 Dec 16  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  4-(Pyridin-3-Yl)-4, 5-Dihydropyrrolo[1, 2-A]Quinoxaline, Dihydropyrrol, Drug, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. You, D. Rotili, T. M. Li, C. Kambach, M. Meleshin, M. Schutkowski, K. F. Chua, A. Mai, C. Steegborn
Structural Basis Of Sirtuin 6 Activation By Synthetic Small Molecules.
Angew. Chem. Int. Ed. Engl. V. 56 1007 2017
PubMed-ID: 27990725  |  Reference-DOI: 10.1002/ANIE.201610082

(-) Compounds

Molecule 1 - NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-6
    ChainsA, B
    EC Number3.5.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET151-D-TOPO
    Expression System Taxid562
    Expression System VariantROSETTA2 (DE3) PLYSS
    Expression System Vector TypePLASMID
    GeneSIRT6, SIR2L6
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymREGULATORY PROTEIN SIR2 HOMOLOG 6,SIR2-LIKE PROTEIN 6

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 18)

Asymmetric Unit (6, 18)
No.NameCountTypeFull Name
17M22Ligand/Ion(4~{R})-4-PYRIDIN-3-YL-4,5-DIHYDROPYRROLO[1,2-A]QUINOXALINE
2AR62Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGENPHOSPHATE
3EDO3Ligand/Ion1,2-ETHANEDIOL
4PGE1Ligand/IonTRIETHYLENE GLYCOL
5SO48Ligand/IonSULFATE ION
6ZN2Ligand/IonZINC ION
Biological Unit 1 (5, 9)
No.NameCountTypeFull Name
17M21Ligand/Ion(4~{R})-4-PYRIDIN-3-YL-4,5-DIHYDROPYRROLO[1,2-A]QUINOXALINE
2AR61Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGENPHOSPHATE
3EDO2Ligand/Ion1,2-ETHANEDIOL
4PGE1Ligand/IonTRIETHYLENE GLYCOL
5SO44Ligand/IonSULFATE ION
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
17M21Ligand/Ion(4~{R})-4-PYRIDIN-3-YL-4,5-DIHYDROPYRROLO[1,2-A]QUINOXALINE
2AR61Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGENPHOSPHATE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4PGE-1Ligand/IonTRIETHYLENE GLYCOL
5SO44Ligand/IonSULFATE ION
6ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:52 , ALA A:53 , GLY A:54 , THR A:57 , ASP A:63 , PHE A:64 , ARG A:65 , TRP A:71 , GLN A:113 , HIS A:133 , GLY A:214 , THR A:215 , SER A:216 , ILE A:219 , ASN A:240 , LEU A:241 , GLN A:242 , GLY A:256 , TYR A:257 , VAL A:258 , PGE A:409 , HOH A:501 , HOH A:508 , HOH A:523 , HOH A:547 , HOH A:579 , HOH A:584 , ASP B:83 , HOH B:521binding site for residue AR6 A 401
02AC2SOFTWARECYS A:141 , CYS A:144 , CYS A:166 , CYS A:177binding site for residue ZN A 402
03AC3SOFTWAREHIS A:68 , LYS A:81 , HOH A:503 , HOH A:507 , HOH A:542 , HIS B:68binding site for residue SO4 A 403
04AC4SOFTWAREVAL A:154 , GLY A:155 , ARG A:164 , LYS A:296binding site for residue SO4 A 404
05AC5SOFTWARELYS A:33 , ARG A:253 , HIS A:255 , HOH A:529binding site for residue SO4 A 405
06AC6SOFTWAREARG A:220 , PRO A:221 , ASN A:224binding site for residue SO4 A 406
07AC7SOFTWAREPHE A:24 , TYR A:257 , HOH A:549 , THR B:84binding site for residue EDO A 407
08AC8SOFTWAREPHE A:82 , THR A:84 , TYR B:257binding site for residue EDO A 408
09AC9SOFTWARELEU A:186 , LEU A:192 , ARG A:220 , AR6 A:401binding site for residue PGE A 409
10AD1SOFTWAREILE A:61 , PRO A:62 , PHE A:64 , PHE A:86 , HOH A:558binding site for residue 7M2 A 410
11AD2SOFTWAREASP A:83 , HOH A:519 , GLY B:52 , ALA B:53 , GLY B:54 , THR B:57 , ASP B:63 , PHE B:64 , ARG B:65 , TRP B:71 , GLN B:113 , HIS B:133 , TRP B:188 , GLY B:214 , THR B:215 , SER B:216 , ILE B:219 , ASN B:240 , LEU B:241 , GLN B:242 , GLY B:256 , TYR B:257 , VAL B:258 , EDO B:407 , HOH B:502 , HOH B:512 , HOH B:537 , HOH B:540 , HOH B:555binding site for residue AR6 B 401
12AD3SOFTWARECYS B:141 , CYS B:144 , CYS B:166 , CYS B:177binding site for residue ZN B 402
13AD4SOFTWAREARG A:90 , ALA A:275 , TRP A:276 , HOH A:513 , ARG B:90 , ALA B:275 , TRP B:276 , HOH B:501 , HOH B:525binding site for residue SO4 B 403
14AD5SOFTWARELYS B:33 , ARG B:253 , HIS B:255 , HOH B:549binding site for residue SO4 B 404
15AD6SOFTWAREVAL B:154 , GLY B:155 , ARG B:164 , LYS B:296binding site for residue SO4 B 405
16AD7SOFTWAREARG B:220 , PRO B:221 , ASN B:224binding site for residue SO4 B 406
17AD8SOFTWARELEU B:186 , ASP B:187 , TRP B:188 , AR6 B:401binding site for residue EDO B 407
18AD9SOFTWAREILE B:61 , PRO B:62 , PHE B:86 , MET B:157 , HOH B:558binding site for residue 7M2 B 408

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5MF6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:220 -Pro A:221
2Arg B:220 -Pro B:221

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5MF6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MF6)

(-) Exons   (0, 0)

(no "Exon" information available for 5MF6)

(-) 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:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhh........hhhhhhhh...............hhhhhhhhhhhhh....eeee....hhhhhh..hhh.eee......eeee.....eee...........eeeee.......eeee.........hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhh.eeeee......hhhhh.eee..hhhhhhhhhhhhh............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5mf6 A  10 PFTADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATGRLCTVACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPKLE 298
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169|      186       196       206       216       226       236       246       256       266       276       286       296  
                                                                                                                                                                                         169|                                                                                                                         
                                                                                                                                                                                          177                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhh........hhhhhhhh...............hhhhhhhhhhhhh....eeee....hhhhheeee...eee......eeee.....eee...........eeeee.......eeee.........hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhh...eeeee......hhhhh.eee..hhhhhhhhhhhhhh.........eee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mf6 B  15 KGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATGRLCTVACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPK 296
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164    || 181       191       201       211       221       231       241       251       261       271       281       291     
                                                                                                                                                                                    169|                                                                                                                       
                                                                                                                                                                                     177                                                                                                                       

   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 5MF6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5MF6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MF6)

(-) Gene Ontology  (35, 35)

Asymmetric Unit(hide GO term definitions)

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        SIR6_HUMAN | Q8N6T73k35 3pki 3pkj 3zg6 5mfp 5mfz 5mgn

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