Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  S65DPARKIN AND PUB COMPLEX
 
Authors :  A. Kumar, V. K. Chaugule, C. Johnson, R. Toth, R. Sundaramoorthy, A. Kne H. Walden
Date :  08 Feb 17  (Deposition) - 19 Apr 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  S65Dparkin Pub Complex, Splicing, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kumar, V. K. Chaugule, T. E. C. Condos, K. R. Barber, C. Johnson, R. Toth, R. Sundaramoorthy, A. Knebel, G. S. Shaw, H. Walden
Parkin-Phosphoubiquitin Complex Reveals Cryptic Ubiquitin-Binding Site Required For Rbr Ligase Activity.
Nat. Struct. Mol. Biol. V. 24 475 2017
PubMed-ID: 28414322  |  Reference-DOI: 10.1038/NSMB.3400

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE PARKIN,E3 UBIQUITIN-PROTEIN LIGASE PARKIN
    Chains: A
    EC Number: 2.3.2.-, 2.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PARK2, PRKN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PARKIN,PARKINSON JUVENILE DISEASE PROTEIN 2,PARKINSON DISEASE PROTEIN 2,PARKIN,PARKINSON JUVENILE DISEASE PROTEIN 2, PARKINSON DISEASE PROTEIN 2
 
Molecule 2 - POLYUBIQUITIN-B
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UBB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: SER65 IS PHOSPHORYLATED

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
13CN1Mod. Amino Acid3-AMINOPROPANE
2CL1Ligand/IonCHLORIDE ION
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4SEP1Mod. Amino AcidPHOSPHOSERINE
5ZN8Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:232 , SER A:233binding site for residue PEG A 2501
02AC2SOFTWARETHR A:237 , CYS A:238 , THR A:242 , ALA A:397binding site for residue CL A 2502
03AC3SOFTWARECYS A:238 , CYS A:241 , CYS A:260 , CYS A:263binding site for residue ZN A 2503
04AC4SOFTWARECYS A:253 , HIS A:257 , CYS A:289 , CYS A:293binding site for residue ZN A 2504
05AC5SOFTWARECYS A:365 , CYS A:368 , HIS A:373 , CYS A:377binding site for residue ZN A 2505
06AC6SOFTWARECYS A:332 , CYS A:337 , CYS A:352 , CYS A:360binding site for residue ZN A 2506
07AC7SOFTWARECYS A:446 , CYS A:449 , CYS A:457 , HIS A:461binding site for residue ZN A 2507
08AC8SOFTWARECYS A:418 , CYS A:421 , CYS A:436 , CYS A:441binding site for residue ZN A 2508
09AC9SOFTWARECYS A:166 , CYS A:169 , CYS A:196 , CYS A:201binding site for residue ZN A 2509
10AD1SOFTWARECYS A:150 , CYS A:154 , CYS A:212 , HIS A:215binding site for residue ZN A 2510

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5N38)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:152 -Pro A:153
2Ser A:246 -Pro A:247
3Gly A:357 -Leu A:358
4Cys A:360 -Gly A:361

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5N38)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5N38)

(-) Exons   (0, 0)

(no "Exon" information available for 5N38)

(-) 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:379
                                                                                                                                                                                                                                                                                                                                                                                                                           
               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.................eee.......eeehhhhhhhhhhhhhhh..eee...eee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee........eeee.....eee...........eee.............hhhhhhhh......eee......eee......eee........eee.......hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5n38 A   1 MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCDLDQQDIVHIVQRPWEMNATNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGECQSPHCPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCITCTDVRSPVLVFQCNSRHVICLDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEPDCRKVTCEGGNGLGCGFAFCRECKEAYHEGECVDERAAEQARWEAKTTKPCPRCHVPVEKNGGCMHMKCPQPQCRLEWCWNCGCEWNRVCMGDHWFDV 465
                                    10        20        30        40        50        60        70   ||  144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374  ||   399     ||416       426       436       446       456         
                                                                                                    74|  83|                                                                                                                                                                                                                                      377|         405|                                                    
                                                                                                     79  144                                                                                                                                                                                                                                       393          413                                                    


Chain B from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeee.....hhhhhhhhhhhhhh.....eeeee..ee......hhhhh.....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 5n38 B   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKEsTLHLVLRLRGg  76
                                    10        20        30        40        50        60    |   70     |
                                                                                           65-SEP     76-3CN
   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 5N38)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5N38)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5N38)

(-) Gene Ontology  (219, 235)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    3CN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SEP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Cys A:360 - Gly A:361   [ RasMol ]  
    Gly A:152 - Pro A:153   [ RasMol ]  
    Gly A:357 - Leu A:358   [ RasMol ]  
    Ser A:246 - Pro A:247   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5n38
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PRKN_HUMAN | O60260
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  UBB_HUMAN | P0CG47
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.3.2.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PRKN_HUMAN | O60260
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  UBB_HUMAN | P0CG47
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PRKN_HUMAN | O60260: 1iyf 2jmo 4bm9 4i1f 4i1h 5c1z 5c23 5c9v 5n2w 5tr5
        UBB_HUMAN | P0CG47: 1c3t 1cmx 1d3z 1f9j 1fxt 1g6j 1gjz 1nbf 1q5w 1s1q 1sif 1tbe 1ubi 1ubq 1ud7 1uzx 1xd3 1yx5 1yx6 1zo6 2ayo 2bgf 2den 2fuh 2g45 2gbj 2gbk 2gbm 2gbn 2gbr 2hth 2ibi 2j7q 2jf5 2jzz 2k6d 2k8b 2k8c 2kdf 2khw 2kjh 2klg 2kn5 2kox 2ktf 2kwu 2kwv 2l0f 2l0t 2mbb 2mro 2msg 2n13 2nr2 2o6v 2ojr 2pe9 2pea 2w9n 2wdt 2xew 2xk5 2y5b 2zcb 3a33 3by4 3c0r 3dvg 3dvn 3eec 3efu 3ehv 3h7p 3h7s 3hm3 3i3t 3ifw 3ihp 3jsv 3jvz 3jw0 3k9p 3kvf 3kw5 3ldz 3mhs 3mtn 3n30 3n32 3n3k 3nhe 3nob 3ns8 3o65 3oj3 3oj4 3ons 3phd 3ptf 3zlz 3znh 4uel 4uf6 4whv 4wlr 4wur 4wzp 4xof 4zfr 4zft 4zpz 4zux 5bnb 5caw 5cra 5cvm 5cvn 5cvo 5d0k 5d0m 5dfl 5dk8 5e6j 5edv 5emz 5eya 5gjq 5go7 5go8 5gob 5goc 5god 5gog 5goh 5goi 5goj 5gok 5ibk 5ifr 5j8p 5jbv 5jby 5jg6 5jp3 5jtj 5jtv 5k9p 5kgf 5khy 5l8h 5l8w 5l9t 5ln1 5lrv 5lrw 5lrx 5m93 5mnj 5n2w 5nl5 5nlj 5nvg 5tof 5tog 5ulf 5ulh 5ulk 5v1y 5v1z 5vey 5vf0 5w46 5x3m 5x3n 5x3o 5xbo 5xdp 5xk4 5xk5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5N38)