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(-) Description

Title :  PARKIN (S65DUBLR0RBR)
 
Authors :  A. Kumar, J. D. Aguirre, T. E. C. Condos, R. J. Martinez-Torres, V. K. Cha R. Toth, R. Sundaramoorthy, P. Mercier, A. Knebel, D. E. Spratt, K. R. B G. S. Shaw, H. Walden
Date :  15 Jun 15  (Deposition) - 29 Jul 15  (Release) - 28 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.37
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  E3 Ligase2, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kumar, J. D. Aguirre, T. E. Condos, R. J. Martinez-Torres, V. K. Chaugule, R. Toth, R. Sundaramoorthy, P. Mercier, A. Knebel, D. E. Spratt, K. R. Barber, G. S. Shaw, H. Walden
Disruption Of The Autoinhibited State Primes The E3 Ligase Parkin For Activation And Catalysis.
Embo J. V. 34 2506 2015
PubMed-ID: 26254304  |  Reference-DOI: 10.15252/EMBJ.201592337

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE PARKIN
    Chains: A, B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: PARK2, PRKN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PARKIN,PARKINSON JUVENILE DISEASE PROTEIN 2,PARKINSON DISEASE 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  (4, 24)

Asymmetric Unit (4, 24)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION
4ZN16Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:150 , CYS A:154 , CYS A:212 , HIS A:215binding site for residue ZN A 501
02AC2SOFTWARECYS A:166 , CYS A:169 , CYS A:196 , CYS A:201binding site for residue ZN A 502
03AC3SOFTWARECYS A:238 , CYS A:241 , CYS A:260 , CYS A:263binding site for residue ZN A 503
04AC4SOFTWARECYS A:253 , HIS A:257 , CYS A:289 , CYS A:293binding site for residue ZN A 504
05AC5SOFTWARECYS A:332 , CYS A:337 , CYS A:352binding site for residue ZN A 505
06AC6SOFTWARECYS A:365 , CYS A:368 , HIS A:373 , CYS A:377binding site for residue ZN A 506
07AC7SOFTWARECYS A:418 , CYS A:421 , CYS A:436 , CYS A:441binding site for residue ZN A 507
08AC8SOFTWARECYS A:446 , CYS A:449 , CYS A:457 , HIS A:461binding site for residue ZN A 508
09AC9SOFTWAREVAL A:186 , LEU A:187 , GLU A:207 , PHE A:208 , HOH A:623binding site for residue GOL A 509
10AD1SOFTWAREHIS A:227 , ALA A:230 , GLN A:252 , ARG A:256 , TRP A:403 , GLU A:404 , VAL A:465 , HOH A:607binding site for residue GOL A 510
11AD2SOFTWAREGLN A:57 , ASN A:58 , LYS A:161 , ARG A:163 , LYS A:211 , THR A:217 , ARG A:455 , HOH A:614 , HOH A:621binding site for residue SO4 A 511
12AD3SOFTWARELYS A:416 , TRP A:447 , ASN A:448binding site for residue SO4 A 512
13AD4SOFTWAREPHE A:146 , TYR A:147 , TRP A:183 , LEU A:226 , ILE A:229binding site for residue CL A 513
14AD5SOFTWARECYS B:150 , CYS B:154 , CYS B:212 , HIS B:215binding site for residue ZN B 501
15AD6SOFTWARECYS B:166 , CYS B:169 , CYS B:196 , CYS B:201binding site for residue ZN B 502
16AD7SOFTWARECYS B:238 , CYS B:241 , CYS B:260 , CYS B:263binding site for residue ZN B 503
17AD8SOFTWARECYS B:253 , HIS B:257 , CYS B:289 , CYS B:293binding site for residue ZN B 504
18AD9SOFTWARECYS B:332 , CYS B:337 , CYS B:352binding site for residue ZN B 505
19AE1SOFTWARECYS B:365 , CYS B:368 , HIS B:373 , CYS B:377binding site for residue ZN B 506
20AE2SOFTWARECYS B:418 , CYS B:421 , CYS B:436 , CYS B:441binding site for residue ZN B 507
21AE3SOFTWARECYS B:446 , CYS B:449 , CYS B:457 , HIS B:461binding site for residue ZN B 508
22AE4SOFTWAREVAL B:186 , GLU B:207 , PHE B:208 , HOH B:602 , HOH B:623binding site for residue GOL B 509
23AE5SOFTWAREHIS B:227 , ALA B:230 , GLN B:252 , ARG B:256 , GLU B:404 , VAL B:465 , HOH B:619binding site for residue GOL B 510
24AE6SOFTWAREASN B:58 , LYS B:161 , ARG B:163 , LYS B:211 , THR B:217 , ARG B:455 , HOH B:613 , HOH B:618 , HOH B:660binding site for residue SO4 B 511

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C23)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:152 -Pro A:153
2Ser A:246 -Pro A:247
3Gly B:152 -Pro B:153
4Ser B:246 -Pro B:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C23)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C23)

(-) Exons   (0, 0)

(no "Exon" information available for 5C23)

(-) 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:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee......eeee.....hhhhhhhhhhhhhh.hhh.eeeee..eee....hhhhhh.....eeeeee...............eeee.....eeeeeeeeeee.......eee.....hhhhhhh.....eee.........eeeeeee...........ee...ee.................eee.......eeehhhhhhhhhhhhhhh..eee...eee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee........ee.......eee......eee....................hhhhhhhh......ee......ee.......eee........eee.......hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5c23 A   1 MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCDLDQQDIVHIVQRPWRKGQEMNATNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGECQSPHCPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCITCTDVRSPVLVFQCNSRHVICLDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEPDQRKVTCEGNGFAFCRECKEAYHEGECSAVFEYRVDERAAEQARWEATTKPCPRCHVPVEKNGGCMHMKCPQPQCRLEWCWNCGCEWNRVCMGDHWFDV 465
                                    10        20        30        40        50        60        70        80  ||   150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350  |||| 365       375      |393       403 ||    421       431       441       451       461    
                                                                                                             83|                                                                                                                                                                                                              353|||                  382|           405|                                                   
                                                                                                             144                                                                                                                                                                                                               355||                   391            414                                                   
                                                                                                                                                                                                                                                                                                                                356|                                                                                        
                                                                                                                                                                                                                                                                                                                                 361                                                                                        


Chain B from PDB  Type:PROTEIN  Length:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee......eeee.....hhhhhhhhhhhhhh.hhh.eeeee..eee...............eeeeee...............eeee.....eeeeeeeeeee.......eee.....hhhhhhh.....eee.........eeeeeee...........ee...ee.................eee.......eeehhhhhhhhhhhhhhh..eee...eee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee........ee.......eee......eee....................hhhhhhhh.....eee......eee......eee........eee.......hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5c23 B   1 MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCDLDQQDIVHIVQRPWRKGQEMNATNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGECQSPHCPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCITCTDVRSPVLVFQCNSRHVICLDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEPDQRKVTCEGNGFAFCRECKEAYHEGECSAVFEYRVDERAAEQARWEATTKPCPRCHVPVEKNGGCMHMKCPQPQCRLEWCWNCGCEWNRVCMGDHWFDV 465
                                    10        20        30        40        50        60        70        80  ||   150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350  |||| 365       375      |393       403 ||    421       431       441       451       461    
                                                                                                             83|                                                                                                                                                                                                              353|||                  382|           405|                                                   
                                                                                                             144                                                                                                                                                                                                               355||                   391            414                                                   
                                                                                                                                                                                                                                                                                                                                356|                                                                                        
                                                                                                                                                                                                                                                                                                                                 361
   Legend:   → Mismatch (orange background)
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    → 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 5C23)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C23)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C23)

(-) Gene Ontology  (146, 146)

Asymmetric Unit(hide GO term definitions)

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  5c23
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  PRKN_HUMAN | O60260
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  6.3.2.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRKN_HUMAN | O60260: 1iyf 2jmo 4bm9 4i1f 4i1h 5c1z 5c9v 5n2w 5n38 5tr5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5C23)