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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SIRT2 IN COMPLEX WITH A SIRREAL PROBE FRAGMENT
 
Authors :  T. Rumpf, S. Gerhardt, O. Einsle, M. Jung
Date :  24 Sep 15  (Deposition) - 20 Jan 16  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (1x)
Keywords :  Hydrolase, Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Schiedel, T. Rumpf, B. Karaman, A. Lehotzky, S. Gerhardt, J. Ovadi, W. Sippl, O. Einsle, M. Jung
Structure-Based Development Of An Affinity Probe For Sirtui 2.
Angew. Chem. Int. Ed. Engl. V. 55 2252 2016
PubMed-ID: 26748890  |  Reference-DOI: 10.1002/ANIE.201509843

(-) Compounds

Molecule 1 - NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2
    Chains: A
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MODIFIED PET15B
    Expression System Taxid: 469008
    Expression System Variant: CODONPLUS RIPL
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 56-356
    Gene: SIRT2, SIR2L, SIR2L2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: GLY53 ORIGINATES FROM THE TEV CLEAVAGE SITE HIS54 AND MET55 ORIGINATE FROM THE NDEI RESTRICTION SITE OF THE VECTOR
    Synonym: REGULATORY PROTEIN SIR2 HOMOLOG 2,SIR2-LIKE PROTEIN 2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 5)

Asymmetric Unit (5, 5)
No.NameCountTypeFull Name
15GR1Ligand/IonN-(5-{3-[(1-BENZYL-1H-1,2,3-TRIAZOL-4-YL)METHOXY]BENZYL}-1,3-THIAZOL-2-YL)-2-[(4,6-DIMETHYLPYRIMIDIN-2-YL)SULFANYL]ACETAMIDE
2BU31Ligand/Ion(R,R)-2,3-BUTANEDIOL
3EDO1Ligand/Ion1,2-ETHANEDIOL
4EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5ZN1Ligand/IonZINC ION
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
15GR2Ligand/IonN-(5-{3-[(1-BENZYL-1H-1,2,3-TRIAZOL-4-YL)METHOXY]BENZYL}-1,3-THIAZOL-2-YL)-2-[(4,6-DIMETHYLPYRIMIDIN-2-YL)SULFANYL]ACETAMIDE
2BU32Ligand/Ion(R,R)-2,3-BUTANEDIOL
3EDO2Ligand/Ion1,2-ETHANEDIOL
4EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
15GR1Ligand/IonN-(5-{3-[(1-BENZYL-1H-1,2,3-TRIAZOL-4-YL)METHOXY]BENZYL}-1,3-THIAZOL-2-YL)-2-[(4,6-DIMETHYLPYRIMIDIN-2-YL)SULFANYL]ACETAMIDE
2BU31Ligand/Ion(R,R)-2,3-BUTANEDIOL
3EDO1Ligand/Ion1,2-ETHANEDIOL
4EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:195 , CYS A:200 , CYS A:221 , CYS A:224binding site for residue ZN A 401
2AC2SOFTWAREPHE A:96 , ARG A:97 , PHE A:119 , PHE A:131 , ALA A:135 , TYR A:139 , PRO A:140 , ILE A:169 , HIS A:187 , PHE A:190 , ILE A:232 , VAL A:233 , PHE A:235 , BU3 A:405 , HOH A:605binding site for residue 5GR A 402
3AC3SOFTWARETHR A:63 , LEU A:64 , GLU A:65 , ALA A:319 , HOH A:508binding site for residue EDO A 403
4AC4SOFTWAREGLU A:61 , THR A:63 , GLU A:65 , ARG A:69 , ARG A:78 , LEU A:252 , LYS A:253 , VAL A:254 , ASP A:255 , HOH A:538binding site for residue EPE A 404
5AC5SOFTWAREALA A:85 , ASP A:95 , PHE A:96 , ARG A:97 , GLN A:167 , ASN A:168 , ILE A:169 , 5GR A:402 , HOH A:505binding site for residue BU3 A 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DY5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:267 -Pro A:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DY5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DY5)

(-) Exons   (0, 0)

(no "Exon" information available for 5DY5)

(-) 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:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhh.....eeeee.hhhhhhhh.........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.......eeehhhhhhhhhh............eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhh.....eeeee........hhhhh.............eeeee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dy5 A  53 GHMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS 356
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292||     306       316       326       336       346       356
                                                                                                                                                                                                                                                                          293|                                                          
                                                                                                                                                                                                                                                                           298
   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 5DY5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DY5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DY5)

(-) Gene Ontology  (117, 117)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        SIR2_HUMAN | Q8IXJ6: 1j8f 3zgo 3zgv 4l3o 4r8m 4rmg 4rmh 4rmi 4rmj 4x3o 4x3p 4y6l 4y6o 4y6q 5d7o 5d7p 5d7q 5dy4 5fyq 5g4c 5mar 5mat

(-) Related Entries Specified in the PDB File

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