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(-) Description

Title :  STRUCTURE OF HUMAN SIRT2 IN COMPLEX WITH 1,2,4-OXADIAZOLE INHIBITOR AND ADP RIBOSE.
 
Authors :  S. Moniot, C. Steegborn
Date :  04 Nov 16  (Deposition) - 15 Mar 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Sirtuin, Nad-Dependent Protein Deacylase, Inhibitor Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Moniot, M. Forgione, A. Lucidi, G. S. Hailu, A. Nebbioso, V. Carafa, F. Baratta, L. Altucci, N. Giacche, D. Passeri, R. Pellicciari, A. Mai C. Steegborn, D. Rotili
Development Of 1, 2, 4-Oxadiazoles As Potent And Selective Inhibitors Of The Human Deacetylase Sirtuin 2: Structure-Activity Relationship, X-Ray Crystal Structure, And Anticancer Activity.
J. Med. Chem. V. 60 2344 2017
PubMed-ID: 28240897  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01609

(-) Compounds

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

 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, 22)

Asymmetric Unit (7, 22)
No.NameCountTypeFull Name
17KE2Ligand/Ion3-[3-(4-CHLOROPHENYL)-1,2,4-OXADIAZOL-5-YL]PROPAN-1-OL
2ACT1Ligand/IonACETATE ION
3AR62Ligand/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
4DMS9Ligand/IonDIMETHYL SULFOXIDE
5EDO2Ligand/Ion1,2-ETHANEDIOL
6GOL4Ligand/IonGLYCEROL
7ZN2Ligand/IonZINC ION
Biological Unit 1 (5, 11)
No.NameCountTypeFull Name
17KE1Ligand/Ion3-[3-(4-CHLOROPHENYL)-1,2,4-OXADIAZOL-5-YL]PROPAN-1-OL
2ACT-1Ligand/IonACETATE ION
3AR61Ligand/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
4DMS5Ligand/IonDIMETHYL SULFOXIDE
5EDO2Ligand/Ion1,2-ETHANEDIOL
6GOL2Ligand/IonGLYCEROL
7ZN-1Ligand/IonZINC ION
Biological Unit 2 (5, 9)
No.NameCountTypeFull Name
17KE1Ligand/Ion3-[3-(4-CHLOROPHENYL)-1,2,4-OXADIAZOL-5-YL]PROPAN-1-OL
2ACT1Ligand/IonACETATE ION
3AR61Ligand/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
4DMS4Ligand/IonDIMETHYL SULFOXIDE
5EDO-1Ligand/Ion1,2-ETHANEDIOL
6GOL2Ligand/IonGLYCEROL
7ZN-1Ligand/IonZINC ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:195 , CYS A:200 , CYS A:221 , CYS A:224binding site for residue ZN A 401
02AC2SOFTWAREGLY A:84 , ALA A:85 , GLY A:86 , THR A:89 , ASP A:95 , PHE A:96 , ARG A:97 , TYR A:104 , GLN A:167 , HIS A:187 , PHE A:235 , GLY A:261 , THR A:262 , SER A:263 , VAL A:266 , ASN A:286 , LYS A:287 , GLU A:288 , GLY A:322 , GLU A:323 , CYS A:324 , 7KE A:403 , EDO A:405 , HOH A:535 , HOH A:545 , HOH A:554 , HOH A:606binding site for residue AR6 A 402
03AC3SOFTWAREPHE A:96 , PHE A:119 , LEU A:134 , LEU A:138 , ILE A:169 , ILE A:232 , VAL A:233 , AR6 A:402 , LEU B:297binding site for residue 7KE A 403
04AC4SOFTWARESER A:311 , ALA A:314binding site for residue EDO A 404
05AC5SOFTWARETHR A:89 , SER A:90 , LYS A:287 , GLU A:323 , AR6 A:402binding site for residue EDO A 405
06AC6SOFTWARETRP A:320 , LEU A:321binding site for residue DMS A 406
07AC7SOFTWAREPHE A:96 , ASN A:168 , ILE A:169 , ASP A:170binding site for residue DMS A 407
08AC8SOFTWAREARG A:77 , ARG A:78 , GLY A:159 , LEU A:161 , LEU A:162binding site for residue DMS A 408
09AC9SOFTWARELEU A:162 , ARG A:163 , GLU A:181 , ASP A:182binding site for residue DMS A 409
10AD1SOFTWAREARG A:75 , TYR A:104 , ASP A:105binding site for residue DMS A 410
11AD2SOFTWAREGLY A:291 , SER A:293 , MET A:299 , MET A:301 , GLY A:302 , GLY A:304 , GLY A:305 , GLY A:306 , HOH A:559binding site for residue GOL A 411
12AD3SOFTWAREARG A:153 , GLU A:348 , SER A:351 , HOH A:507 , CYS B:224binding site for residue GOL A 412
13AD4SOFTWARECYS B:195 , CYS B:200 , CYS B:221 , CYS B:224binding site for residue ZN B 401
14AD5SOFTWAREGLY B:84 , ALA B:85 , GLY B:86 , THR B:89 , ASP B:95 , PHE B:96 , ARG B:97 , TYR B:104 , GLN B:167 , HIS B:187 , PHE B:235 , GLY B:261 , THR B:262 , SER B:263 , VAL B:266 , ASN B:286 , LYS B:287 , GLU B:288 , GLY B:322 , GLU B:323 , CYS B:324 , 7KE B:403 , HOH B:533 , HOH B:547 , HOH B:548binding site for residue AR6 B 402
15AD6SOFTWAREPHE B:96 , PHE B:119 , LEU B:134 , LEU B:138 , ILE B:169 , ILE B:232 , VAL B:233 , AR6 B:402binding site for residue 7KE B 403
16AD7SOFTWAREALA B:319 , TRP B:320 , LEU B:321binding site for residue ACT B 404
17AD8SOFTWAREPHE B:96 , ASN B:168 , ILE B:169 , ASP B:170binding site for residue DMS B 405
18AD9SOFTWAREARG B:77 , GLY B:159 , LEU B:161binding site for residue DMS B 406
19AE1SOFTWARELEU B:162 , ARG B:163 , GLU B:181 , ASP B:182binding site for residue DMS B 407
20AE2SOFTWAREHOH A:556 , HOH A:701 , TYR B:114 , GOL B:409binding site for residue DMS B 408
21AE3SOFTWAREGLU B:116 , DMS B:408binding site for residue GOL B 409
22AE4SOFTWARESER A:73 , GLU A:74 , CYS A:76 , ARG A:77 , SER B:122 , TYR B:123 , LYS B:126 , HOH B:558 , HOH B:598binding site for residue GOL B 410

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:267 -Pro A:268
2Gln B:267 -Pro B:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MAR)

(-) 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:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhh......eeeee.hhhhhhhh.........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.......eeehhhhhhhhh.............eeeee.......hhhhhhhhhhhh....eeeee.......hhhhhhhhh.....eeeee..............................eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mar A  54 HMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ 355
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353  


Chain B from PDB  Type:PROTEIN  Length:302
                                                                                                                                                                                                                                                                                                                                              
               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.......hhhhhhhhhhhh....eeeee.......hhhhhhhhh.....eeeee..............................eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mar B  54 HMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ 355
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353
   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 5MAR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (117, 117)

Asymmetric Unit(hide GO term definitions)

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

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