PDB entry 2nvu

View 2nvu on RCSB PDB site
Description: Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like protein activation complex
Class: protein turnover, ligase
Keywords: Multifunction macromolecular complex, Ubiquitin, NEDD8, E1, E2, ATP, Conformational change, thioester, switch, adenylation, PROTEIN TURNOVER, LIGASE
Deposited on 2006-11-13, released 2007-01-30
The last revision prior to the SCOPe 2.03 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 2.8 Å
R-factor: 0.241
AEROSPACI score: 0.23 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: NEDD8-activating enzyme E1 regulatory subunit
    Species: Homo sapiens [TaxId:9606]
    Gene: APPBP1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d2nvua_
  • Chain 'B':
    Compound: Maltose binding protein/NEDD8-activating enzyme E1 catalytic subunit chimera
    Species: Homo sapiens [TaxId:9606]
    Gene: UBE1C, UBA3
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8TBC4 (374-804)
      • see remark 999 (373)
    Domains in SCOPe 2.03: d2nvub1, d2nvub2
  • Chain 'C':
    Compound: NEDD8-conjugating enzyme Ubc12
    Species: Homo sapiens [TaxId:9606]
    Gene: UBE2M, UBC12
    Database cross-references and differences (RAF-indexed):
    • Uniprot P61081 (Start-174)
      • engineered (107)
    Domains in SCOPe 2.03: d2nvuc1
  • Chain 'I':
    Compound: nedd8
    Species: Homo sapiens [TaxId:9606]
    Gene: NEDD8
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d2nvui_
  • Chain 'J':
    Compound: nedd8
    Species: Homo sapiens [TaxId:9606]
    Gene: NEDD8
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d2nvuj_
  • Heterogens: MG, ZN, ATP, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2nvuA (A:)
    gsmaqlgkllkeqkydrqlrlwgdhgqealesahvclinatatgteilknlvlpgigsft
    iidgnqvsgedagnnfflqrssigknraeaameflqelnsdvsgsfveespenlldndps
    ffcrftvvvatqlpestslrladvlwnsqipllicrtyglvgymriiikehpvieshpdn
    aledlrldkpfpelrehfqsydldhmekkdhshtpwiviiakylaqwysetngripktyk
    ekedfrdlirqgilknengapedeenfeeaiknvntalnttqipssiedifnddrcinit
    kqtpsfwilaralkefvakegqgnlpvrgtipdmiadsgkyiklqnvyrekakkdaaavg
    nhvakllqsigqapesisekelkllcsnsaflrvvrcrslaeeygldtinkdeiissmdn
    pdneivlylmlravdrfhkqqgrypgvsnyqveedigklkscltgflqeyglsvmvkddy
    vhefcrygaaephtiaaflggaaaqevikiitkqfvifnntyiysgmsqtsatfql
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nvuA (A:)
    gkllkeqkydrqlrlwgdhgqealesahvclinatatgteilknlvlpgigsftiidgnq
    vsgedagnnfflqrssigknraeaameflqelnsdvsgsfveespenlldndpsffcrft
    vvvatqlpestslrladvlwnsqipllicrtyglvgymriiikehpvieshpdnaledlr
    ldkpfpelrehfqsydldhmekkdhshtpwiviiakylaqwysetngripktykekedfr
    dlirqgilknengapedeenfeeaiknvntalnttqipssiedifnddrcinitkqtpsf
    wilaralkefvakegqgnlpvrgtipdmiadsgkyiklqnvyrekakkdaaavgnhvakl
    lqsigqapesisekelkllcsnsaflrvvrcrslaeeygldtinkdeiissmdnpdneiv
    lylmlravdrfhkqqgrypgvsnyqveedigklkscltgflqeyglsvmvkddyvhefcr
    ygaaephtiaaflggaaaqevikiitkqfvifnntyiysgmsqtsatfql
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2nvuB (B:)
    mklmkieegklviwingdkgynglaevgkkfekdtgikvtvehpdkleekfpqvaatgdg
    pdiifwahdrfggyaqsgllaeitpdkafqdklypftwdavryngkliaypiavealsli
    ynkdllpnppktweeipaldkelkakgksalmfnlqepyftwpliaadggyafkyengky
    dikdvgvdnagakagltflvdliknkhmnadtdysiaeaafnkgetamtingpwawsnid
    tskvnygvtvlptfkgqpskpfvgvlsaginaaspnkelakeflenylltdegleavnkd
    kplgavalksyeeelakdpriaatmenaqkgeimpnipqmsafwyavrtavinaasgrqt
    vdaalaaaqtnaaadwegrwnhvkkflersgpfthpdfepsteslqflldtckvlvigag
    glgcellknlalsgfrqihvidmdtidvsnlnrqflfrpkdigrpkaevaaeflndrvpn
    cnvvphfnkiqdfndtfyrqfhiivcgldsiiarrwingmlisllnyedgvldpssivpl
    idggtegfkgnarvilpgmtaciectlelyppqvnfpmctiasmprlpehcieyvrmlqw
    pkeqpfgegvpldgddpehiqwifqkslerasqynirgvtyrltqgvvkriipavastna
    viaavcatevfkiatsayiplnnylvfndvdglytytfeaerkencpacsqlpqniqfsp
    saklqevldyltnsaslqmkspaitatlegknrtlylqsvtsieertrpnlsktlkelgl
    vdgqelavadvttpqtvlfklhfts
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nvuB (B:)
    kieegklviwingdkgynglaevgkkfekdtgikvtvehpdkleekfpqvaatgdgpdii
    fwahdrfggyaqsgllaeitpdkafqdklypftwdavryngkliaypiavealsliynkd
    llpnppktweeipaldkelkakgksalmfnlqepyftwpliaadggyafkyengkydikd
    vgvdnagakagltflvdliknkhmnadtdysiaeaafnkgetamtingpwawsnidtskv
    nygvtvlptfkgqpskpfvgvlsaginaaspnkelakeflenylltdegleavnkdkval
    ksyeeeatmenaqkgeimpnipqmsafwyavrtavinaasgrqtvdaalaaaqtnaaadw
    egrwnhvkkflersgpfthpdfepsteslqflldtckvlvigagglgcellknlalsgfr
    qihvidmdtidvsnlnrqflfrpkdigrpkaevaaeflndrvpncnvvphfnkiqdfndt
    fyrqfhiivcgldsiiarrwingmlisllnyedgvldpssivplidggtegfkgnarvil
    pgmtaciectlelyppqvnfpmctiasmprlpehcieyvrmlqwpkeqpfgegvpldgdd
    pehiqwifqkslerasqynirgvtyrltqgvvkriipavastnaviaavcatevfkiats
    ayiplnnylvfndvdglytytfeaerkencpacsqlpqniqfspsaklqevldyltnsas
    lqmkspaitatlegknrtlylqsvtsieertrpnlsktlkelglvdgqelavadvttpqt
    vlfklhfts
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2nvuC (C:)
    gsmiklfslkqqkkeeekgsskkasaaqlriqkdinelnlpktcdisfsdpddllnfklv
    icpdegfyksgkfvfsfkvgqgyphdppkvkcetmvyhpnidlegnvalnilredwkpvl
    tinsiiyglqylflepnpedplnkeaaevlqnnrrlfeqnvqrsmrggyigstyferclk
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nvuC (C:)
    klfslkqqkkeeekgsskkasaaqlriqkdinelnlpktcdisfsdpddllnfklvicpd
    egfyksgkfvfsfkvgqgyphdppkvkcetmvyhpnidlegnvalnilredwkpvltins
    iiyglqylflepnpedplnkeaaevlqnnrrlfeqnvqrsmrggyigstyferclk
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >2nvuI (I:)
    gsggsmlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndekt
    aadykilggsvlhlvlalrgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nvuI (I:)
    mlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndektaadyk
    ilggsvlhlvlalrgg
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >2nvuJ (J:)
    gsggsmlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndekt
    aadykilggsvlhlvlalrgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nvuJ (J:)
    mlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndektaadyk
    ilggsvlhlvlalrgg