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(-) Description

Title :  STRUCTURE OF HUMAN PARKIN G319A
 
Authors :  T. Wauer, D. Komander
Date :  29 Jun 15  (Deposition) - 22 Jul 15  (Release) - 26 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Parkin, Ubiquitin, E3 Ligase, Rbr, Parkinson'S Disease, Mitophagy, Cell Signalling, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Wauer, M. Simicek, A. Schubert, D. Komander
Mechanism Of Phospho-Ubiquitin-Induced Parkin Activation.
Nature V. 524 370 2015
PubMed-ID: 26161729  |  Reference-DOI: 10.1038/NATURE14879
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE PARKIN
    ChainsA
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System PlasmidPOPINK
    Expression System Taxid866768
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 137-465
    GenePARK2, PRKN
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsENGINEERED MUTATION AT POSITION G319A
    SynonymPARKIN,PARKINSON JUVENILE DISEASE PROTEIN 2,PARKINSON DISEASE PROTEIN 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric/Biological Unit (3, 17)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION
3ZN8Ligand/IonZINC ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:150 , CYS A:154 , CYS A:212 , HIS A:215binding site for residue ZN A 501
02AC2SOFTWARECYS A:253 , HIS A:257 , CYS A:289 , CYS A:293binding site for residue ZN A 502
03AC3SOFTWARECYS A:446 , CYS A:449 , CYS A:457 , HIS A:461binding site for residue ZN A 503
04AC4SOFTWARECYS A:166 , CYS A:169 , CYS A:196 , CYS A:201binding site for residue ZN A 504
05AC5SOFTWARECYS A:238 , CYS A:241 , CYS A:260 , CYS A:263binding site for residue ZN A 505
06AC6SOFTWARECYS A:332 , CYS A:337 , CYS A:352 , CYS A:360binding site for residue ZN A 506
07AC7SOFTWARECYS A:365 , CYS A:368 , HIS A:373 , CYS A:377binding site for residue ZN A 507
08AC8SOFTWARECYS A:418 , CYS A:421 , CYS A:436 , CYS A:441binding site for residue ZN A 508
09AC9SOFTWAREARG A:163 , LYS A:211 , THR A:217 , ARG A:420 , HOH A:624binding site for residue SO4 A 509
10AD1SOFTWAREASN A:454 , ARG A:455binding site for residue SO4 A 510
11AD2SOFTWAREHIS A:279 , ARG A:334 , GLY A:361binding site for residue SO4 A 511
12AD3SOFTWAREASN A:254 , PRO A:294binding site for residue SO4 A 512
13AD4SOFTWARELYS A:151 , HIS A:302 , ARG A:305 , TYR A:312 , HOH A:603binding site for residue SO4 A 513
14AD5SOFTWAREARG A:348 , TYR A:372binding site for residue SO4 A 514
15AD6SOFTWARECYS A:368 , HIS A:373 , GLU A:376 , CYS A:377 , SER A:378binding site for residue GOL A 515
16AD7SOFTWAREVAL A:186 , LEU A:187 , PRO A:189 , PHE A:208 , HOH A:604 , HOH A:621binding site for residue GOL A 516
17AD8SOFTWAREASN A:295 , SER A:296 , LEU A:297binding site for residue GOL A 517

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C9V)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:152 -Pro A:153
2Ser A:246 -Pro A:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C9V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C9V)

(-) Exons   (0, 0)

(no "Exon" information available for 5C9V)

(-) 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee.....eeeeeeeeeee.......eee.....hhhhhhh.....eee.........eeeeeee...........ee...ee.................eee.......eeehhhhhhhhhhhhhh...eee...eee.............hhhhhhhhhhhhhhhhhhhhhhhhhhh...ee........ee.......eee........eee............hhhhhh....hhhhhhhh....eee......eee......eee........eee.......hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5c9v A 142 IYNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGECQSPHCPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCITCTDVRSPVLVFQCNSRHVICLDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQYAAEECVLQMGGVLCPRPGCGAGLLPEPDQRKVTCEGLGCGFAFCRECKEAYHEGECSAVFEASYRVDERAAEQARWETTKPCPRCHVPVEKNGGCMHMKCPQPQCRLEWCWNCGCEWNRVCMGDHWFDV 465
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351 ||    364       374       384|      400   ||  419       429       439       449       459      
                                                                                                                                                                                                                                             353|                        384|          404|                                                   
                                                                                                                                                                                                                                              357                         391           414                                                   

   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 5C9V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C9V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C9V)

(-) Gene Ontology  (146, 146)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:152 - Pro A:153   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRKN_HUMAN | O602601iyf 2jmo 4bm9 4i1f 4i1h 5c1z 5c23 5n2w 5n38 5tr5

(-) Related Entries Specified in the PDB File

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