PDB entry 3dbl

View 3dbl on RCSB PDB site
Description: Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190wt-NEDD8Ala72Gln)
Class: cell cycle
Keywords: Cell cycle, activating enzyme, Apoptosis, Membrane, Ubl conjugation pathway, ATP-binding, Ligase, Nucleotide-binding, Polymorphism, Nucleus
Deposited on 2008-06-01, released 2008-08-12
The last revision prior to the SCOPe 2.03 freeze date was dated 2009-07-14, with a file datestamp of 2009-07-10.
Experiment type: XRAY
Resolution: 2.9 Å
R-factor: 0.225
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: NAE1, APPBP1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d3dbla_
  • 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 (207)
    Domains in SCOPe 2.03: d3dblb_
  • 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 2.03: d3dblc_
  • 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 (3-433)
      • expression tag (2)
      • engineered (207)
    Domains in SCOPe 2.03: d3dbld_
  • 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 2.03: d3dble_
  • 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 (207)
    Domains in SCOPe 2.03: d3dblf_
  • 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 2.03: d3dblg_
  • 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 (207)
    Domains in SCOPe 2.03: d3dblh_
  • Chain 'I':
    Compound: nedd8
    Species: Homo sapiens [TaxId:9606]
    Gene: NEDD8
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15843 (12-87)
      • expression tag (2-11)
      • engineered (83)
    Domains in SCOPe 2.03: d3dbli_
  • Chain 'J':
    Compound: nedd8
    Species: Homo sapiens [TaxId:9606]
    Gene: NEDD8
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15843 (12-87)
      • engineered (83)
    Domains in SCOPe 2.03: d3dblj_
  • Chain 'K':
    Compound: nedd8
    Species: Homo sapiens [TaxId:9606]
    Gene: NEDD8
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15843 (12-87)
      • engineered (83)
    Domains in SCOPe 2.03: d3dblk_
  • Chain 'L':
    Compound: nedd8
    Species: Homo sapiens [TaxId:9606]
    Gene: NEDD8
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15843 (12-87)
      • engineered (83)
    Domains in SCOPe 2.03: d3dbll_
  • Heterogens: ZN

PDB Chain Sequences:

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

    Sequence, based on observed residues (ATOM records): (download)
    >3dblA (A:)
    kllkeqkydrqlrlwgdhgqealesahvclinatatgteilknlvlpgigsftiidgnqv
    sgedagnnfflqrssigknraeaameflqelnsdvsgsfveespenlldndpsffcrftv
    vvatqlpestslrladvlwnsqipllicrtyglvgymriiikehpvieshpdnaledlrl
    dkpfpelrehfqsydldhmkdhshtpwiviiakylaqwysetngripktykekedfrdli
    rqgilkpedeenfeeaiknvntalnttqipssiedifnddrcinitkqtpsfwilaralk
    efvakegqgnlpvrgtipdmiadsgkyiklqnvyrekakkdaaavgnhvakllqsigqap
    esisekelkllcsnsaflrvvrcrslaeeygldtinkdeiissmdnpdneivlylmlrav
    drfhkqqgrypgvsnyqveedigklkscltgflqeyglsvmvkddyvhefcrygaaepht
    iaaflggaaaqevikiitkqfvifnntyiysgmsqtsatfql
    

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

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

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

    Sequence, based on observed residues (ATOM records): (download)
    >3dblC (C:)
    kllkeqkydrqlrlwgdhgqealesahvclinatatgteilknlvlpgigsftiidgnqv
    sgedagnnfflqrssigknraeaameflqelnsdvsgsfveespenlldndpsffcrftv
    vvatqlpestslrladvlwnsqipllicrtyglvgymriiikehpvieshpdnaledlrl
    dkpfpelrehfqsyddmedhshtpwiviiakylaqwysetngripktykekedfrdlirq
    gilkpedeenfeeaiknvntalnttqipssiedifnddrcinitkqtpsfwilaralkef
    vakegqgnlpvrgtipdmiadsgkyiklqnvyrekakkdaaavgnhvakllqsigqapes
    isekelkllcsnsaflrvvrcrslaeeygldtinkdeiissmdnpdneivlylmlravdr
    fhkqqgrypgvsnyqveedigklkscltgflqeyglsvmvkddyvhefcrygaaephtia
    aflggaaaqevikiitkqfvifnntyiysgmsqtsatfql
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >3dblD (D:)
    ldwegrwnhvkkflersgpfthpdfepsteslqflldtckvlvigagglgcellknlals
    gfrqihvidmdtidvsnlnrqflfrpkdigrpkaevaaeflndrvpncnvvphfnkiqdf
    ndtfyrqfhiivcgldsiiarrwingmlisllnyedgvldpssivplidggtegfkgnar
    vilpgmtaciectlelyppqvnfpmatiasmprlpehcieyvrmlqwpkeqpfgegvpld
    gddpehiqwifqkslerasqynirgvtyrltqgvvkriipavastnaviaavcatevfki
    atsayiplnnylvfndvdglytytfeaerkencpacsqlpqniqfspsaklqevldyltn
    saslqmkspaitatlegknrtlylqsvtsieertrpnlsktlkelglvdgqelavadvtt
    pqtvlfklhfts
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >3dblE (E:)
    kllkeqkydrqlrlwgdhgqealesahvclinatatgteilknlvlpgigsftiidgnqv
    sgedagnnfflqrssigknraeaameflqelnsdvsgsfveespenlldndpsffcrftv
    vvatqlpestslrladvlwnsqipllicrtyglvgymriiikehpvieshpdnaledlrl
    dkpfpelrehfqsydldhekkdhshtpwiviiakylaqwysetngripktykekedfrdl
    irqgilkpeenfeeaiknvntalnttqipssiedifnddrcinitkqtpsfwilaralke
    fvakegqgnlpvrgtipdmiadsgkyiklqnvyrekakkdaaavgnhvakllqsigqape
    sisekelkllcsnsaflrvvrcrslaeeygldtinkdeiissmdnpdneivlylmlravd
    rfhkqqgrypgvsnyqveedigklkscltgflqeyglsvmvkddyvhefcrygaaephti
    aaflggaaaqevikiitkqfvifnntyiysgmsqtsatfql
    

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

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

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

    Sequence, based on observed residues (ATOM records): (download)
    >3dblG (G:)
    kllkeqkydrqlrlwgdhgqealesahvclinatatgteilknlvlpgigsftiidgnqv
    sgedagnnfflqrssigknraeaameflqelnsdvsgsfveespenlldndpsffcrftv
    vvatqlpestslrladvlwnsqipllicrtyglvgymriiikehpvieshpdnaledlrl
    dkpfpelrehfqsydldhdhshtpwiviiakylaqwysetngripktykekedfrdlirq
    gilkdeenfeeaiknvntalnttqipssiedifnddrcinitkqtpsfwilaralkefva
    kegqgnlpvrgtipdmiadsgkyiklqnvyrekakkdaaavgnhvakllqsigqapesis
    ekelkllcsnsaflrvvrcrslaeeygldtinkdeiissmdnpdneivlylmlravdrfh
    kqqgrypgvsnyqveedigklkscltgflqeyglsvmvkddyvhefcrygaaephtiaaf
    lggaaaqevikiitkqfvifnntyiysgmsqtsatfql
    

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

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

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

    Sequence, based on observed residues (ATOM records): (download)
    >3dblI (I:)
    rrasvgsggsmlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqm
    ndektaadykilggsvlhlvlqlrgg
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >3dblJ (J:)
    mlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndektaadyk
    ilggsvlhlvlqlrgg
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >3dblK (K:)
    mlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndektaadyk
    ilggsvlhlvlqlrgg
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >3dblL (L:)
    mlikvktltgkeieidieptdkverikerveekegippqqqrliysgkqmndektaadyk
    ilggsvlhlvlqlrgg