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(-) Description

Title :  CRYSTAL STRUCTURE OF SIRT5 IN COMPLEX WITH A COUMARIN-LABELLED SUCCINYL PEPTIDE
 
Authors :  W. Gai, H. Jiang, D. Liu
Date :  08 Jun 15  (Deposition) - 13 Jul 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Gai, H. Jiang, D. Liu
Crystal Structure Of Sirt5 In Complex With A Coumarin-Labelled Succinyl Peptide
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
    Chains: A
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 33-302
    Gene: SIRT5, SIR2L5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: REGULATORY PROTEIN SIR2 HOMOLOG 5,SIR2-LIKE PROTEIN 5
 
Molecule 2 - COUMARIN-LABELLED SUCCINYL PEPTIDE
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1MCM1Ligand/Ion7-AMINO-4-METHYL-CHROMEN-2-ONE
2SLL1Mod. Amino Acid(2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL)AMINO]HEXANOIC ACID
3ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:166 , CYS A:169 , CYS A:207 , CYS A:212binding site for residue ZN A 401
2AC2SOFTWAREARG A:71 , ALA A:86 , TYR A:102 , ARG A:105 , ILE A:142 , VAL A:221 , TRP A:222 , PHE A:223 , GLY A:224 , GLU A:225 , TYR A:255 , HOH A:543 , HOH A:595 , GLY B:2 , HOH B:201 , HOH B:203binding site for residues MCM B 101 and SLL B 3

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:178 -Pro A:179
2Tyr A:255 -Pro A:256
3Thr A:279 -Pro A:280
4Pro A:280 -Ala A:281

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BWL)

(-) 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:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.eeeeeehhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...eeeeee....hhhhhh....eee..eeeeeeee.....eee......hhhhh..............hhhhh...........eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhh...eeeee...........eeee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bwl A  36 PSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA 302
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       


Chain B from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 5bwl B   1 LGx   3
                              |
                              3-SLL
   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 5BWL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Pro A:280 - Ala A:281   [ RasMol ]  
    Ser A:178 - Pro A:179   [ RasMol ]  
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    Tyr A:255 - Pro A:256   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        SIR5_HUMAN | Q9NXA8: 2b4y 2nyr 3rig 3riy 4f4u 4f56 4g1c 4hda

(-) Related Entries Specified in the PDB File

5bwn 5bwo 5bwp 5bwq