Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF HUMAN SIRTUIN 2 IN COMPLEX WITH A SELECTIVE THIENOPYRIMIDINONE BASED INHIBITOR
 
Authors :  S. Moniot, C. Steegborn
Date :  04 Nov 16  (Deposition) - 08 Feb 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Nad-Dependent Protein Deacylase, Sirtuin, Inhibitor Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sundriyal, S. Moniot, Z. Mahmud, S. Yao, P. Di Fruscia, C. R. Reynolds, D. T. Dexter, M. J. Sternberg, E. W. Lam, C. Steegborn, M. J. Fuchter
Thienopyrimidinone Based Sirtuin-2 (Sirt2)-Selective Inhibitors Bind In The Ligand Induced Selectivity Pocket.
J. Med. Chem. V. 60 1928 2017
PubMed-ID: 28135086  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01690

(-) Compounds

Molecule 1 - NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2
    Chains: A, C
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET19 MODIFIED
    Expression System Taxid: 511693
    Expression System Variant: CODON PLUS
    Gene: SIRT2, SIR2L, SIR2L2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: N-TERMINAL RESIDUES HM ARE CLONING ARTIFACTS
    Synonym: REGULATORY PROTEIN SIR2 HOMOLOG 2,SIR2-LIKE PROTEIN 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 19)

Asymmetric/Biological Unit (5, 19)
No.NameCountTypeFull Name
17KJ1Ligand/Ion(7~{R})-7-[(3,5-DIMETHYL-1,2-OXAZOL-4-YL)METHYLAMINO]-3-[(4-METHOXYNAPHTHALEN-1-YL)METHYL]-5,6,7,8-TETRAHYDRO-[1]BENZOTHIOLO[2,3-D]PYRIMIDIN-4-ONE
2P6G1Ligand/IonHEXAETHYLENE GLYCOL
3PG41Ligand/IonTETRAETHYLENE GLYCOL
4SO414Ligand/IonSULFATE ION
5ZN2Ligand/IonZINC ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:195 , CYS A:200 , CYS A:221 , CYS A:224binding site for residue ZN A 401
02AC2SOFTWAREILE A:93 , PRO A:94 , PHE A:96 , PHE A:119 , ALA A:135 , LEU A:138 , TYR A:139 , PHE A:143 , ILE A:169 , THR A:171 , PHE A:190 , VAL A:233 , PHE A:235 , HOH A:632 , HOH A:646binding site for residue 7KJ A 402
03AC3SOFTWAREGLY A:84 , ALA A:85 , GLN A:167 , THR A:262 , SER A:263 , VAL A:266 , HOH A:508 , HOH A:537 , HOH A:586binding site for residue SO4 A 403
04AC4SOFTWAREALA A:290 , GLY A:291 , GLN A:292 , SER A:293 , HOH A:574binding site for residue SO4 A 404
05AC5SOFTWAREPRO A:277 , LEU A:278 , SER A:279 , HOH A:724binding site for residue SO4 A 405
06AC6SOFTWARELYS A:158 , TRP A:337 , HOH A:653binding site for residue SO4 A 406
07AC7SOFTWAREGLN A:292 , HOH A:546 , HOH A:568binding site for residue SO4 A 407
08AC8SOFTWAREPRO A:240 , ALA A:241 , HOH A:668binding site for residue SO4 A 408
09AC9SOFTWAREARG A:78 , LYS A:253 , HOH A:690binding site for residue SO4 A 409
10AD1SOFTWAREGLU A:333 , GLY A:336 , TRP A:337 , LYS A:338 , LYS A:339 , HOH A:610 , HOH A:669binding site for residue SO4 A 410
11AD2SOFTWARELEU A:329 , LYS A:338 , GLU A:342 , HOH A:511 , HOH A:623binding site for residue PG4 A 411
12AD3SOFTWARECYS C:195 , CYS C:200 , CYS C:221 , CYS C:224binding site for residue ZN C 401
13AD4SOFTWARESER A:274 , ALA A:276 , GLY A:304 , GLY A:305 , ALA C:276 , LEU C:278 , GLY C:302 , LEU C:303 , GLY C:304 , GLY C:305 , TYR C:315 , ARG C:316 , HOH C:521 , HOH C:532binding site for residue P6G C 402
14AD5SOFTWAREALA C:290 , GLY C:291 , GLN C:292 , SER C:293 , HOH C:537 , HOH C:570binding site for residue SO4 C 403
15AD6SOFTWAREALA C:332 , GLU C:333 , GLY C:336 , TRP C:337 , LYS C:338 , LYS C:339 , HOH C:556binding site for residue SO4 C 404
16AD7SOFTWARELYS C:312 , HOH C:575 , HOH C:660binding site for residue SO4 C 405
17AD8SOFTWAREPRO C:240 , ALA C:241 , HOH C:602binding site for residue SO4 C 406
18AD9SOFTWAREARG C:97 , THR C:262 , SER C:263 , LEU C:264 , GLN C:265 , VAL C:266 , HOH C:501 , HOH C:518 , HOH C:526binding site for residue SO4 C 407
19AE1SOFTWAREARG C:78 , LYS C:253 , HOH C:614binding site for residue SO4 C 408

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:267 -Pro A:268
2Gln C:267 -Pro C:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MAT)

(-) Sequences/Alignments

Asymmetric/Biological 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 ........hhhhhhhhhh......eeeee.hhhhhhhh.........hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.......eeehhhhhhhhhh............eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhh.....eeeee..............................eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5mat A  55 MERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS 356
                                    64        74        84        94   ||  106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356
                                                                      98|                                                                                                                                                                                                                                                               
                                                                      101                                                                                                                                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhh.....eeeee.hhhhhhhh......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.......eeehhhhhhhhhh............eeeee.......hhhhhhhhhhhh....eeeee.......hhhhhhhhh.....eeeee..............................eeeee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mat C  54 HMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS 356
                                    63        73        83        93    || 108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348        
                                                                       98|                                                                                                                                                                                                                                                            
                                                                       104
   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 5MAT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (117, 117)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    7KJ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    P6G  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
    AD7  [ RasMol ]  +environment [ RasMol ]
    AD8  [ RasMol ]  +environment [ RasMol ]
    AD9  [ RasMol ]  +environment [ RasMol ]
    AE1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln A:267 - Pro A:268   [ RasMol ]  
    Gln C:267 - Pro C:268   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5mat
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SIR2_HUMAN | Q8IXJ6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.5.1.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SIR2_HUMAN | Q8IXJ6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SIR2_HUMAN | Q8IXJ6: 1j8f 3zgo 3zgv 4l3o 4r8m 4rmg 4rmh 4rmi 4rmj 4x3o 4x3p 4y6l 4y6o 4y6q 5d7o 5d7p 5d7q 5dy4 5dy5 5fyq 5g4c 5mar

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5MAT)