PDB entry 3dbr

View 3dbr on RCSB PDB site
Description: Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Gln-NEDD8Ala72Arg)
Class: Cell Cycle
Keywords: cell cycle, activating enzyme, Apoptosis, Membrane, Ubl conjugation pathway, ATP-binding, Ligase, Nucleotide-binding, Polymorphism, Nucleus
Deposited on 2008-06-02, released 2008-08-12
The last revision prior to the SCOPe 2.04 freeze date was dated 2009-07-14, with a file datestamp of 2009-07-10.
Experiment type: XRAY
Resolution: 3.05 Å
R-factor: 0.23
AEROSPACI score: 0.2 (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: NAE1, APPBP1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d3dbra_
  • Chain 'B':
    Compound: NEDD8-activating enzyme E1 catalytic subunit
    Species: Homo sapiens [TaxId:9606]
    Gene: UBA3, UBE1C
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8TBC4 (3-433)
      • expression tag (2)
      • engineered (181)
      • engineered (207)
    Domains in SCOPe 2.04: d3dbrb_
  • Chain 'C':
    Compound: NEDD8-activating enzyme E1 regulatory subunit
    Species: Homo sapiens [TaxId:9606]
    Gene: NAE1, APPBP1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d3dbrc_
  • Chain 'D':
    Compound: NEDD8-activating enzyme E1 catalytic subunit
    Species: Homo sapiens [TaxId:9606]
    Gene: UBA3, UBE1C
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8TBC4 (3-End)
      • expression tag (2)
      • engineered (181)
      • engineered (207)
    Domains in SCOPe 2.04: d3dbrd_
  • Chain 'E':
    Compound: NEDD8-activating enzyme E1 regulatory subunit
    Species: Homo sapiens [TaxId:9606]
    Gene: NAE1, APPBP1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d3dbre_
  • Chain 'F':
    Compound: NEDD8-activating enzyme E1 catalytic subunit
    Species: Homo sapiens [TaxId:9606]
    Gene: UBA3, UBE1C
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8TBC4 (3-End)
      • expression tag (2)
      • engineered (181)
      • engineered (207)
    Domains in SCOPe 2.04: d3dbrf_
  • Chain 'G':
    Compound: NEDD8-activating enzyme E1 regulatory subunit
    Species: Homo sapiens [TaxId:9606]
    Gene: NAE1, APPBP1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.04: d3dbrg_
  • Chain 'H':
    Compound: NEDD8-activating enzyme E1 catalytic subunit
    Species: Homo sapiens [TaxId:9606]
    Gene: UBA3, UBE1C
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q8TBC4 (3-End)
      • expression tag (2)
      • engineered (181)
      • engineered (207)
    Domains in SCOPe 2.04: d3dbrh_
  • Chain 'I':
    Compound: nedd8
    Species: Homo sapiens [TaxId:9606]
    Gene: NEDD8
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15843 (12-87)
      • expression tag (2-8)
      • expression tag (10-11)
      • engineered (83)
    Domains in SCOPe 2.04: d3dbri_
  • Chain 'J':
    Compound: nedd8
    Species: Homo sapiens [TaxId:9606]
    Gene: NEDD8
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15843 (12-87)
      • expression tag (11)
      • engineered (83)
    Domains in SCOPe 2.04: d3dbrj_
  • Chain 'K':
    Compound: nedd8
    Species: Homo sapiens [TaxId:9606]
    Gene: NEDD8
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15843 (12-87)
      • expression tag (11)
      • engineered (83)
    Domains in SCOPe 2.04: d3dbrk_
  • Chain 'L':
    Compound: nedd8
    Species: Homo sapiens [TaxId:9606]
    Gene: NEDD8
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15843 (12-87)
      • expression tag (10-11)
      • engineered (83)
    Domains in SCOPe 2.04: d3dbrl_
  • Heterogens: ZN

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3dbrA (A:)
    gsmaqlgkllkeqkydrqlrlwgdhgqealesahvclinatatgteilknlvlpgigsft
    iidgnqvsgedagnnfflqrssigknraeaameflqelnsdvsgsfveespenlldndps
    ffcrftvvvatqlpestslrladvlwnsqipllicrtyglvgymriiikehpvieshpdn
    aledlrldkpfpelrehfqsydldhmekkdhshtpwiviiakylaqwysetngripktyk
    ekedfrdlirqgilkpedeenfeeaiknvntalnttqipssiedifnddrcinitkqtps
    fwilaralkefvakegqgnlpvrgtipdmiadsgkyiklqnvyrekakkdaaavgnhvak
    llqsigqapesisekelkllcsnsaflrvvrcrslaeeygldtinkdeiissmdnpdnei
    vlylmlravdrfhkqqgrypgvsnyqveedigklkscltgflqeyglsvmvkddyvhefc
    rygaaephtiaaflggaaaqevikiitkqfvifnntyiysgmsqtsatfql
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dbrA (A:)
    kllkeqkydrqlrlwgdhgqealesahvclinatatgteilknlvlpgigsftiidgnqv
    sgedagnnfflqrssigknraeaameflqelnsdvsgsfveespenlldndpsffcrftv
    vvatqlpestslrladvlwnsqipllicrtyglvgymriiikehpvieshpdnaledlrl
    dkpfpelrehfqsyddhshtpwiviiakylaqwysetngripktykekedfrdlirqgil
    kpedeenfeeaiknvntalnttqipssiedifnddrcinitkqtpsfwilaralkefvak
    egqgnlpvrgtipdmiadsgkyiklqnvyrekakkdaaavgnhvakllqsigqapesise
    kelkllcsnsaflrvvrcrslaeeygldtinkdeiissmdnpdneivlylmlravdrfhk
    qqgrypgvsnyqveedigklkscltgflqeyglsvmvkddyvhefcrygaaephtiaafl
    ggaaaqevikiitkqfvifnntyiysgmsqtsatfql
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3dbrB (B:)
    mkldwegrwnhvkkflersgpfthpdfepsteslqflldtckvlvigagglgcellknla
    lsgfrqihvidmdtidvsnlnrqflfrpkdigrpkaevaaeflndrvpncnvvphfnkiq
    dfndtfyrqfhiivcgldsiiarrwingmlisllnyedgvldpssivplidggtegfkgn
    aqvilpgmtaciectlelyppqvnfpmatiasmprlpehcieyvrmlqwpkeqpfgegvp
    ldgddpehiqwifqkslerasqynirgvtyrltqgvvkriipavastnaviaavcatevf
    kiatsayiplnnylvfndvdglytytfeaerkencpacsqlpqniqfspsaklqevldyl
    tnsaslqmkspaitatlegknrtlylqsvtsieertrpnlsktlkelglvdgqelavadv
    ttpqtvlfklhfts
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dbrB (B:)
    ldwegrwnhvkkflersgpfthpdfepsteslqflldtckvlvigagglgcellknlals
    gfrqihvidmdtidvsnlnrqflfrpkdigrpkaevaaeflndrvpncnvvphfnkiqdf
    ndtfyrqfhiivcgldsiiarrwingmlisllnyedgvldpssivplidggtegfkgnaq
    vilpgmtaciectlelyppqvnfpmatiasmprlpehcieyvrmlqwpkeqpfgegvpld
    gddpehiqwifqkslerasqynirgvtyrltqgvvkriipavastnaviaavcatevfki
    atsayiplnnylvfndvdglytytfeaerkencpacsqlpqniqfspsaklqevldyltn
    saslqmkspaitatlegknrtlylqsvtsieertrpnlsktlkelglvdgqelavadvtt
    pqtvlfklhfts
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3dbrC (C:)
    gsmaqlgkllkeqkydrqlrlwgdhgqealesahvclinatatgteilknlvlpgigsft
    iidgnqvsgedagnnfflqrssigknraeaameflqelnsdvsgsfveespenlldndps
    ffcrftvvvatqlpestslrladvlwnsqipllicrtyglvgymriiikehpvieshpdn
    aledlrldkpfpelrehfqsydldhmekkdhshtpwiviiakylaqwysetngripktyk
    ekedfrdlirqgilkpedeenfeeaiknvntalnttqipssiedifnddrcinitkqtps
    fwilaralkefvakegqgnlpvrgtipdmiadsgkyiklqnvyrekakkdaaavgnhvak
    llqsigqapesisekelkllcsnsaflrvvrcrslaeeygldtinkdeiissmdnpdnei
    vlylmlravdrfhkqqgrypgvsnyqveedigklkscltgflqeyglsvmvkddyvhefc
    rygaaephtiaaflggaaaqevikiitkqfvifnntyiysgmsqtsatfql
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dbrC (C:)
    kllkeqkydrqlrlwgdhgqealesahvclinatatgteilknlvlpgigsftiidgnqv
    sgedagnnfflqrssigknraeaameflqelnsdvsgsfveespenlldndpsffcrftv
    vvatqlpestslrladvlwnsqipllicrtyglvgymriiikehpvieshpdnaledlrl
    dkpfpelrehfqsydhshtpwiviiakylaqwysetngripktykekedfrdlirqgilk
    pedeenfeeaiknvntalnttqipssiedifnddrcinitkqtpsfwilaralkefvake
    gqgnlpvrgtipdmiadsgkyiklqnvyrekakkdaaavgnhvakllqsigqapesisek
    elkllcsnsaflrvvrcrslaeeygldtinkdeiissmdnpdneivlylmlravdrfhkq
    qgrypgvsnyqveedigklkscltgflqeyglsvmvkddyvhefcrygaaephtiaaflg
    gaaaqevikiitkqfvifnntyiysgmsqtsatfql
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3dbrD (D:)
    mkldwegrwnhvkkflersgpfthpdfepsteslqflldtckvlvigagglgcellknla
    lsgfrqihvidmdtidvsnlnrqflfrpkdigrpkaevaaeflndrvpncnvvphfnkiq
    dfndtfyrqfhiivcgldsiiarrwingmlisllnyedgvldpssivplidggtegfkgn
    aqvilpgmtaciectlelyppqvnfpmatiasmprlpehcieyvrmlqwpkeqpfgegvp
    ldgddpehiqwifqkslerasqynirgvtyrltqgvvkriipavastnaviaavcatevf
    kiatsayiplnnylvfndvdglytytfeaerkencpacsqlpqniqfspsaklqevldyl
    tnsaslqmkspaitatlegknrtlylqsvtsieertrpnlsktlkelglvdgqelavadv
    ttpqtvlfklhfts
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dbrD (D:)
    ldwegrwnhvkkflersgpfthpdfepsteslqflldtckvlvigagglgcellknlals
    gfrqihvidmdtidvsnlnrqflfrpkdigrpkaevaaeflndrvpncnvvphfnkiqdf
    ndtfyrqfhiivcgldsiiarrwingmlisllnyedgvldpssivplidggtegfkgnaq
    vilpgmtaciectlelyppqvnfpmatiasmprlpehcieyvrmlqwpkeqpfgegvpld
    gddpehiqwifqkslerasqynirgvtyrltqgvvkriipavastnaviaavcatevfki
    atsayiplnnylvfndvdglytytfeaerkencpacsqlpqniqfspsaklqevldyltn
    saslqmkspaitatlegknrtlylqsvtsieertrpnlsktlkelglvdgqelavadvtt
    pqtvlfklhft
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3dbrE (E:)
    gsmaqlgkllkeqkydrqlrlwgdhgqealesahvclinatatgteilknlvlpgigsft
    iidgnqvsgedagnnfflqrssigknraeaameflqelnsdvsgsfveespenlldndps
    ffcrftvvvatqlpestslrladvlwnsqipllicrtyglvgymriiikehpvieshpdn
    aledlrldkpfpelrehfqsydldhmekkdhshtpwiviiakylaqwysetngripktyk
    ekedfrdlirqgilkpedeenfeeaiknvntalnttqipssiedifnddrcinitkqtps
    fwilaralkefvakegqgnlpvrgtipdmiadsgkyiklqnvyrekakkdaaavgnhvak
    llqsigqapesisekelkllcsnsaflrvvrcrslaeeygldtinkdeiissmdnpdnei
    vlylmlravdrfhkqqgrypgvsnyqveedigklkscltgflqeyglsvmvkddyvhefc
    rygaaephtiaaflggaaaqevikiitkqfvifnntyiysgmsqtsatfql
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dbrE (E:)
    kllkeqkydrqlrlwgdhgqealesahvclinatatgteilknlvlpgigsftiidgnqv
    sgedagnnfflqrssigknraeaameflqelnsdvsgsfveespenlldndpsffcrftv
    vvatqlpestslrladvlwnsqipllicrtyglvgymriiikehpvieshpdnaledlrl
    dkpfpelrehfqsydlhtpwiviiakylaqwysetngripktykekedfrdlirqgilkp
    edeenfeeaiknvntalnttqipssiedifnddrcinitkqtpsfwilaralkefvakeg
    qgnlpvrgtipdmiadsgkyiklqnvyrekakkdaaavgnhvakllqsigqapesiseke
    lkllcsnsaflrvvrcrslaeeygldtinkdeiissmdnpdneivlylmlravdrfhkqq
    grypgvsnyqveedigklkscltgflqeyglsvmvkddyvhefcrygaaephtiaaflgg
    aaaqevikiitkqfvifnntyiysgmsqtsatfql
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3dbrF (F:)
    mkldwegrwnhvkkflersgpfthpdfepsteslqflldtckvlvigagglgcellknla
    lsgfrqihvidmdtidvsnlnrqflfrpkdigrpkaevaaeflndrvpncnvvphfnkiq
    dfndtfyrqfhiivcgldsiiarrwingmlisllnyedgvldpssivplidggtegfkgn
    aqvilpgmtaciectlelyppqvnfpmatiasmprlpehcieyvrmlqwpkeqpfgegvp
    ldgddpehiqwifqkslerasqynirgvtyrltqgvvkriipavastnaviaavcatevf
    kiatsayiplnnylvfndvdglytytfeaerkencpacsqlpqniqfspsaklqevldyl
    tnsaslqmkspaitatlegknrtlylqsvtsieertrpnlsktlkelglvdgqelavadv
    ttpqtvlfklhfts
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dbrF (F:)
    ldwegrwnhvkkflersgpfthpdfepsteslqflldtckvlvigagglgcellknlals
    gfrqihvidmdtidvsnlnrqflfrpkdigrpkaevaaeflndrvpncnvvphfnkiqdf
    ndtfyrqfhiivcgldsiiarrwingmlisllnyedgvldpssivplidggtegfkgnaq
    vilpgmtaciectlelyppqvnfpmatiasmprlpehcieyvrmlqwpkeqpfgegvpld
    gddpehiqwifqkslerasqynirgvtyrltqgvvkriipavastnaviaavcatevfki
    atsayiplnnylvfndvdglytytfeaerkencpacsqlpqniqfspsaklqevldyltn
    saslqmkspaitatlegknrtlylqsvtsieertrpnlsktlkelglvdgqelavadvtt
    pqtvlfklhft
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >3dbrG (G:)
    gsmaqlgkllkeqkydrqlrlwgdhgqealesahvclinatatgteilknlvlpgigsft
    iidgnqvsgedagnnfflqrssigknraeaameflqelnsdvsgsfveespenlldndps
    ffcrftvvvatqlpestslrladvlwnsqipllicrtyglvgymriiikehpvieshpdn
    aledlrldkpfpelrehfqsydldhmekkdhshtpwiviiakylaqwysetngripktyk
    ekedfrdlirqgilkpedeenfeeaiknvntalnttqipssiedifnddrcinitkqtps
    fwilaralkefvakegqgnlpvrgtipdmiadsgkyiklqnvyrekakkdaaavgnhvak
    llqsigqapesisekelkllcsnsaflrvvrcrslaeeygldtinkdeiissmdnpdnei
    vlylmlravdrfhkqqgrypgvsnyqveedigklkscltgflqeyglsvmvkddyvhefc
    rygaaephtiaaflggaaaqevikiitkqfvifnntyiysgmsqtsatfql
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dbrG (G:)
    kllkeqkydrqlrlwgdhgqealesahvclinatatgteilknlvlpgigsftiidgnqv
    sgedagnnfflqrssigknraeaameflqelnsdvsgsfveespenlldndpsffcrftv
    vvatqlpestslrladvlwnsqipllicrtyglvgymriiikehpvieshpdnaledlrl
    dkpfpelrehfqsytpwiviiakylaqwysetngripktykekedfrdlirqgileenfe
    eaiknvntalnttqipssiedifnddrcinitkqtpsfwilaralkefvakegqgnlpvr
    gtipdmiadsgkyiklqnvyrekakkdaaavgnhvakllqsigqapesisekelkllcsn
    saflrvvrcrslaeeygldtinkdeiissmdnpdneivlylmlravdrfhkqqgrypgvs
    nyqveedigklkscltgflqeyglsvmvkddyvhefcrygaaephtiaaflggaaaqevi
    kiitkqfvifnntyiysgmsqtsatfql
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >3dbrH (H:)
    mkldwegrwnhvkkflersgpfthpdfepsteslqflldtckvlvigagglgcellknla
    lsgfrqihvidmdtidvsnlnrqflfrpkdigrpkaevaaeflndrvpncnvvphfnkiq
    dfndtfyrqfhiivcgldsiiarrwingmlisllnyedgvldpssivplidggtegfkgn
    aqvilpgmtaciectlelyppqvnfpmatiasmprlpehcieyvrmlqwpkeqpfgegvp
    ldgddpehiqwifqkslerasqynirgvtyrltqgvvkriipavastnaviaavcatevf
    kiatsayiplnnylvfndvdglytytfeaerkencpacsqlpqniqfspsaklqevldyl
    tnsaslqmkspaitatlegknrtlylqsvtsieertrpnlsktlkelglvdgqelavadv
    ttpqtvlfklhfts
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dbrH (H:)
    ldwegrwnhvkkflersgpfthpdfepsteslqflldtckvlvigagglgcellknlals
    gfrqihvidmdtidvsnlnrqflfrpkdigrpkaevaaeflndrvpncnvvphfnkiqdf
    ndtfyrqfhiivcgldsiiarrwingmlisllnyedgvldpssivplidggtegfkgnaq
    vilpgmtaciectlelyppqvnfpmatiasmprlpehcieyvrmlqwpkeqpfgegvpld
    gddpehiqwifqkslerasqynirgvtyrltqgvvkriipavastnaviaavcatevfki
    atsayiplnnylvfndvdglytytfeaerkencpacsqlpqniqfspsaklqevldyltn
    saslqmkspaitatlegknrtlylqsvtsieertrpnlsktlkelglvdgqelavadvtt
    pqtvlfklhft
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >3dbrI (I:)
    gsrrasvgsggsmlikvktltgkeieidieptdkverikerveekegippqqqrliysgk
    qmndektaadykilggsvlhlvlrlrgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dbrI (I:)
    rrasvgsgsmlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmn
    dektaadykilggsvlhlvlrlrgg
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >3dbrJ (J:)
    gsrrasvgsggsmlikvktltgkeieidieptdkverikerveekegippqqqrliysgk
    qmndektaadykilggsvlhlvlrlrgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dbrJ (J:)
    smlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndektaady
    kilggsvlhlvlrlrgg
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >3dbrK (K:)
    gsrrasvgsggsmlikvktltgkeieidieptdkverikerveekegippqqqrliysgk
    qmndektaadykilggsvlhlvlrlrgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dbrK (K:)
    smlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndektaady
    kilggsvlhlvlrlrgg
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >3dbrL (L:)
    gsrrasvgsggsmlikvktltgkeieidieptdkverikerveekegippqqqrliysgk
    qmndektaadykilggsvlhlvlrlrgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dbrL (L:)
    gsmlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndektaad
    ykilggsvlhlvlrlrgg