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(-) Description

Title :  HUMAN SIRT5 BOUND TO SUCC-IDH2 AND CARBA-NAD
 
Authors :  H. Dai
Date :  10 Jul 12  (Deposition) - 15 Aug 12  (Release) - 19 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  A,B,D,E  (1x)
Keywords :  Sirtuin, Succinylated Peptide, Carbanad, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. G. Szczepankiewicz, H. Dai, K. J. Koppetsch, D. Qian, F. Jiang, C. Mao, R. B. Perni
Synthesis Of Carba-Nad And The Structures Of Its Ternary Complexes With Sirt3 And Sirt5.
J. Org. Chem. V. 77 7319 2012
PubMed-ID: 22849721  |  Reference-DOI: 10.1021/JO301067E

(-) Compounds

Molecule 1 - NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
    Chains: A, B
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 36-302
    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 - SUCCINYLATED IDH2 PEPTIDE
    Chains: D, E
    Engineered: YES
    Other Details: SYNTHETIC SUCC-IDH2 PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDE
Biological Unit 1 (1x): A D 
Biological Unit 2 (1x):  B E
Biological Unit 3 (1x): ABDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric Unit (5, 9)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2CNA1Ligand/IonCARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3NH22Mod. Amino AcidAMINO GROUP
4SLL2Mod. Amino Acid(2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL)AMINO]HEXANOIC ACID
5ZN2Ligand/IonZINC ION
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CNA1Ligand/IonCARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3NH21Mod. Amino AcidAMINO GROUP
4SLL1Mod. Amino Acid(2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL)AMINO]HEXANOIC ACID
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2CNA-1Ligand/IonCARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3NH21Mod. Amino AcidAMINO GROUP
4SLL1Mod. Amino Acid(2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL)AMINO]HEXANOIC ACID
5ZN-1Ligand/IonZINC ION
Biological Unit 3 (4, 7)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2CNA1Ligand/IonCARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3NH22Mod. Amino AcidAMINO GROUP
4SLL2Mod. Amino Acid(2S)-2-AZANYL-6-[(4-HYDROXY-4-OXO-BUTANOYL)AMINO]HEXANOIC ACID
5ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:166 , CYS A:169 , CYS A:207 , CYS A:212BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREALA A:59 , GLY A:60 , ALA A:63 , GLU A:64 , VAL A:67 , PRO A:68 , THR A:69 , PHE A:70 , ARG A:71 , GLN A:140 , ASN A:141 , ILE A:142 , ASP A:143 , HIS A:158 , GLY A:249 , THR A:250 , SER A:251 , ASN A:275 , THR A:276 , GLU A:277 , PRO A:292 , CYS A:293 , HOH A:550 , HOH A:561 , HOH A:568 , SLL D:3BINDING SITE FOR RESIDUE CNA A 402
3AC3SOFTWARECYS B:166 , CYS B:169 , CYS B:207 , CYS B:212BINDING SITE FOR RESIDUE ZN B 401

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1D:4 -E:4

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:178 -Pro A:179
2Tyr A:255 -Pro A:256
3Ser B:178 -Pro B:179
4Tyr B:255 -Pro B:256

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G1C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G1C)

(-) Exons   (0, 0)

(no "Exon" information available for 4G1C)

(-) 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:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.eeeeee.hhhhhh......hhhh.ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhh...eee..eeeeeeee.....eee......hhhhh..............hhhhh...........eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhh...eeeee.....hhhhh.eeee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g1c 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:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.eeeeeehhhhhhhhh.........ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhh...eee..eeeeeeee.....eee......hhhhh..............hhhhh...........eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhh...eeeee.....hhhhh.eeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g1c B  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 D from PDB  Type:PROTEIN  Length:7
                                       
               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
                 4g1c D   0 xAVkCAx   6
                            |  |  |
                            0-ACE |
                               3-SLL
                                  6-NH2


Chain E from PDB  Type:PROTEIN  Length:7
                                       
               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
                 4g1c E   0 xAVkCAx   6
                            |  |  |
                            |  |  |
                            0-ACE |
                               3-SLL
                                  6-NH2
   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 4G1C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G1C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G1C)

(-) Gene Ontology  (28, 28)

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        SIR5_HUMAN | Q9NXA8: 2b4y 2nyr 3rig 3riy 4f4u 4f56 4hda 5bwl

(-) Related Entries Specified in the PDB File

4fvt