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(-) Description

Title :  HUMAN SIRT6 IN COMPLEX WITH ACTIVATOR UBCS58
 
Authors :  C. Steegborn, W. You, C. Kambach
Date :  18 Nov 16  (Deposition) - 28 Dec 16  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  4-(Pyridin-3-Yl)Pyrrolo[1, 2-A]Quinoxaline, 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
    Chains: A, B
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET151-D-TOPO
    Expression System Strain: ROSETTA2 (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SIRT6, SIR2L6
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: REGULATORY 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  (7, 21)

Asymmetric Unit (7, 21)
No.NameCountTypeFull Name
17M52Ligand/Ion4-PYRIDIN-3-YLPYRROLO[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
3EDO4Ligand/Ion1,2-ETHANEDIOL
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5PGE1Ligand/IonTRIETHYLENE GLYCOL
6SO49Ligand/IonSULFATE ION
7ZN2Ligand/IonZINC ION
Biological Unit 1 (5, 10)
No.NameCountTypeFull Name
17M51Ligand/Ion4-PYRIDIN-3-YLPYRROLO[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
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5PGE-1Ligand/IonTRIETHYLENE GLYCOL
6SO45Ligand/IonSULFATE ION
7ZN-1Ligand/IonZINC ION
Biological Unit 2 (5, 9)
No.NameCountTypeFull Name
17M51Ligand/Ion4-PYRIDIN-3-YLPYRROLO[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
4PG4-1Ligand/IonTETRAETHYLENE GLYCOL
5PGE1Ligand/IonTRIETHYLENE GLYCOL
6SO44Ligand/IonSULFATE ION
7ZN-1Ligand/IonZINC ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
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 , PG4 A:410 , HOH A:505 , HOH A:514 , HOH A:540 , HOH A:556 , HOH A:563 , HOH A:584 , HOH A:585 , ASP B:83binding site for residue AR6 A 401
02AC2SOFTWARECYS A:141 , CYS A:144 , CYS A:166 , CYS A:177binding site for residue ZN A 402
03AC3SOFTWAREARG A:90 , ALA A:275 , TRP A:276 , HOH A:502 , HOH A:562 , ARG B:90 , ALA B:275 , TRP B:276binding site for residue SO4 A 403
04AC4SOFTWAREVAL A:154 , GLY A:155 , THR A:162 , ARG A:164 , LYS A:296binding site for residue SO4 A 404
05AC5SOFTWARELYS A:33 , ARG A:253 , HIS A:255 , HOH A:531binding site for residue SO4 A 405
06AC6SOFTWAREARG A:220 , PRO A:221 , ASN A:224binding site for residue SO4 A 406
07AC7SOFTWAREARG A:205 , ARG A:231 , ARG A:232 , ARG B:205 , ARG B:231binding site for residue SO4 A 407
08AC8SOFTWARETYR B:257binding site for residue EDO A 408
09AC9SOFTWARETYR A:257binding site for residue EDO A 409
10AD1SOFTWARELEU A:186 , TRP A:188 , ASP A:190 , LEU A:192 , ARG A:220 , AR6 A:401 , 7M5 A:411 , HOH A:523binding site for residue PG4 A 410
11AD2SOFTWAREILE A:61 , PRO A:62 , PHE A:64 , PG4 A:410 , HOH A:571 , HOH A:599binding site for residue 7M5 A 411
12AD3SOFTWAREASP A:83 , HOH A:518 , 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 , PGE B:407 , HOH B:505 , HOH B:525 , HOH B:537 , HOH B:553 , HOH B:567binding site for residue AR6 B 401
13AD4SOFTWARECYS B:141 , CYS B:144 , CYS B:166 , CYS B:177binding site for residue ZN B 402
14AD5SOFTWAREHIS A:68 , LYS A:81 , HOH A:507 , HIS B:68 , LYS B:81 , HOH B:503 , HOH B:517binding site for residue SO4 B 403
15AD6SOFTWARELYS B:33 , ARG B:253 , HIS B:255binding site for residue SO4 B 404
16AD7SOFTWAREVAL B:154 , GLY B:155 , THR B:162 , ARG B:164 , LYS B:296binding site for residue SO4 B 405
17AD8SOFTWAREPRO B:221 , ASN B:224binding site for residue SO4 B 406
18AD9SOFTWARETRP B:188 , ASP B:190 , LEU B:192 , ILE B:219 , ARG B:220 , AR6 B:401binding site for residue PGE B 407
19AE1SOFTWAREARG B:103 , PRO B:287 , LEU B:289 , HOH B:551 , HOH B:575binding site for residue EDO B 408
20AE2SOFTWAREARG B:103 , PRO B:290binding site for residue EDO B 409
21AE3SOFTWAREPRO B:62 , PHE B:64 , PHE B:82 , PHE B:86 , MET B:157 , HOH B:555 , HOH B:574binding site for residue 7M5 B 410

(-) SS Bonds  (0, 0)

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

(-) 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 5MFP)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MFP)

(-) 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..hhhhhhhhhhhhhh............................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5mfp 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........hhhhhhh................hhhhhhhhhhhhh....eeee....hhhhhh..hhh.eee......eeee.....eee...........eeeee.......eeee.........hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhh...eeeee......hhhhh.eee..hhhhhhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mfp 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)
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  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 5MFP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (35, 35)

Asymmetric Unit(hide GO term definitions)

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  5mfp
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        SIR6_HUMAN | Q8N6T7: 3k35 3pki 3pkj 3zg6 5mf6 5mfz 5mgn

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