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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SIRT3 AT AN IMPROVED RESOLUTION
 
Authors :  T. Rumpf, S. Gerhardt, O. Einsle, M. Jung
Date :  14 Aug 15  (Deposition) - 02 Dec 15  (Release) - 09 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Hydrolase, Sirtuin 3, Deacylase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Rumpf, S. Gerhardt, O. Einsle, M. Jung
Seeding For Sirtuins: Microseed Matrix Seeding To Obtain Crystals Of Human Sirt3 And Sirt2 Suitable For Soaking.
Acta Crystallogr. , Sect. F V. 71 1498 2015
PubMed-ID: 26625292  |  Reference-DOI: 10.1107/S2053230X15019986

(-) Compounds

Molecule 1 - NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
    Chains: A, B, C, D, E, F
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 118-395
    Gene: SIRT3, SIR2L3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: GLY1 ORIGINATES FROM TEV CLEAVAGE SITE HIS2/MET3 ORIGINATE FROM NDEI RESTRICTION SITE OF THE VECTOR
    Synonym: HSIRT3,REGULATORY PROTEIN SIR2 HOMOLOG 3,SIR2-LIKE PROTEIN 3

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 17)

Asymmetric Unit (7, 17)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2GOL1Ligand/IonGLYCEROL
3MG1Ligand/IonMAGNESIUM ION
4PEG6Ligand/IonDI(HYDROXYETHYL)ETHER
5PG41Ligand/IonTETRAETHYLENE GLYCOL
6PGE1Ligand/IonTRIETHYLENE GLYCOL
7ZN6Ligand/IonZINC ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2GOL-1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
5PG4-1Ligand/IonTETRAETHYLENE GLYCOL
6PGE-1Ligand/IonTRIETHYLENE GLYCOL
7ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2GOL-1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5PG4-1Ligand/IonTETRAETHYLENE GLYCOL
6PGE-1Ligand/IonTRIETHYLENE GLYCOL
7ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2GOL-1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5PG4-1Ligand/IonTETRAETHYLENE GLYCOL
6PGE-1Ligand/IonTRIETHYLENE GLYCOL
7ZN-1Ligand/IonZINC ION
Biological Unit 4 (3, 3)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2GOL1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5PG4-1Ligand/IonTETRAETHYLENE GLYCOL
6PGE-1Ligand/IonTRIETHYLENE GLYCOL
7ZN-1Ligand/IonZINC ION
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2GOL-1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
5PG4-1Ligand/IonTETRAETHYLENE GLYCOL
6PGE1Ligand/IonTRIETHYLENE GLYCOL
7ZN-1Ligand/IonZINC ION
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2GOL-1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
5PG41Ligand/IonTETRAETHYLENE GLYCOL
6PGE-1Ligand/IonTRIETHYLENE GLYCOL
7ZN-1Ligand/IonZINC ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:256 , CYS A:259 , CYS A:280 , CYS A:283binding site for residue ZN A 401
02AC2SOFTWAREVAL A:292 , PHE A:293 , HOH A:633binding site for residue PEG A 402
03AC3SOFTWARECYS A:259 , GLN A:260binding site for residue PEG A 404
04AC4SOFTWAREHOH A:680 , GLU F:375 , HOH F:571 , HOH F:584 , HOH F:628 , HOH F:645binding site for residue MG A 405
05AC5SOFTWARECYS B:256 , CYS B:259 , CYS B:280 , CYS B:283binding site for residue ZN B 401
06AC6SOFTWAREHIS B:248 , VAL B:292 , PHE B:293 , PHE B:294 , HOH B:502 , HOH B:561binding site for residue PEG B 402
07AC7SOFTWARECYS C:256 , CYS C:259 , CYS C:280 , CYS C:283binding site for residue ZN C 401
08AC8SOFTWAREPHE C:180 , HIS C:248 , VAL C:292 , HOH C:650binding site for residue PEG C 402
09AC9SOFTWARECYS D:256 , CYS D:259 , CYS D:280 , CYS D:283binding site for residue ZN D 401
10AD1SOFTWAREGLU D:323 , GOL D:404 , HOH D:690 , GLU F:181binding site for residue PEG D 402
11AD2SOFTWAREGLN D:228 , HIS D:248 , VAL D:292 , PHE D:294 , GLY D:295binding site for residue 1PE D 403
12AD3SOFTWARELEU D:322 , GLU D:323 , GLU D:325 , PEG D:402 , TYR F:175 , GLU F:177binding site for residue GOL D 404
13AD4SOFTWARECYS E:256 , CYS E:259 , CYS E:280 , CYS E:283binding site for residue ZN E 401
14AD5SOFTWAREARG E:158 , PHE E:180 , HIS E:248 , VAL E:292 , PHE E:294 , GLY E:295binding site for residue PGE E 402
15AD6SOFTWARECYS F:256 , CYS F:259 , CYS F:280 , CYS F:283binding site for residue ZN F 401
16AD7SOFTWAREARG F:158 , GLN F:228 , HIS F:248 , VAL F:292 , PHE F:294 , HOH F:502 , HOH F:505 , HOH F:570 , HOH F:617 , HOH F:636binding site for residue PG4 F 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D7N)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Glu A:325 -Pro A:326
2Glu B:325 -Pro B:326
3Glu C:325 -Pro C:326
4Glu D:325 -Pro D:326
5Glu E:325 -Pro E:326
6Glu F:325 -Pro F:326

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D7N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D7N)

(-) Exons   (0, 0)

(no "Exon" information available for 5D7N)

(-) 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:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh.....eeeee.hhhhhhhh........hhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.....eee...hhhhhhh............eeeee.......hhhhhhhhhhhhhh.eeeee........hhhhhhhh.....eeeee...hhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7n A 121 GKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRET 391
                                   130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390 


Chain B from PDB  Type:PROTEIN  Length:272
                                                                                                                                                                                                                                                                                                                
               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.....eee...hhhhhhh............eeeee.......hhhhhhhhhhhhhh.eeeee........hhhhhhh......eeeee...hhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7n B 122 KLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGK 393
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391  


Chain C from PDB  Type:PROTEIN  Length:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh.....eeeee.hhhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.....eee...hhhhhhh............eeeee.......hhhhhhhhhhhhhh.eeeee.......hhhhhh........eeeee....hhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7n C 121 GKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETG 392
                                   130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390  


Chain D from PDB  Type:PROTEIN  Length:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh.....eeeee.hhhhhhhh........hhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.....eee...hhhhhhh............eeeee.......hhhhhhhhhhhhhh.eeeee........hhhhhhh......eeeee...hhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7n D 121 GKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETG 392
                                   130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390  


Chain E from PDB  Type:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.....eeeee.hhhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.....eee...hhhhhhh............eeeee.......hhhhhhhhhhhhhh.eeeee........hhhhhhh......eeeee...hhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7n E 122 KLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETG 392
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 


Chain F from PDB  Type:PROTEIN  Length:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.....eeeee.hhhhhhhh........hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.....eee...hhhhhhh............eeeee.......hhhhhhhhhhhhhh.eeeee........hhhhhhh......eeeee...hhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5d7n F 122 KLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRET 391
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391
   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 5D7N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D7N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D7N)

(-) Gene Ontology  (19, 19)

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  5d7n
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(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SIR3_HUMAN | Q9NTG7: 3glr 3gls 3glt 3glu 4bn4 4bn5 4bv3 4bvb 4bve 4bvf 4bvg 4bvh 4c78 4c7b 4fvt 4fz3 4hd8 4jsr 4jt8 4jt9 4o8z 4v1c 5bwn 5bwo

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5D7N)