PDB entry 3dbh

View 3dbh on RCSB PDB site
Description: Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Ala-NEDD8Ala72Arg)
Class: cell cycle
Keywords: Cell cycle, activating enzyme, Apoptosis, Membrane, Ubl conjugation pathway, ATP-binding, Ligase, Nucleotide-binding, Polymorphism, Nucleus
Deposited on 2008-05-31, released 2008-08-12
The last revision prior to the SCOPe 2.07 freeze date was dated 2009-06-09, with a file datestamp of 2009-06-05.
Experiment type: XRAY
Resolution: 2.85 Å
R-factor: 0.224
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 2.07: d3dbha_
  • 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 2.07: d3dbhb1, d3dbhb2
  • 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 2.07: d3dbhc_
  • 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 (181)
      • engineered (207)
    Domains in SCOPe 2.07: d3dbhd1, d3dbhd2
  • 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 2.07: d3dbhe_
  • 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 2.07: d3dbhf1, d3dbhf2
  • 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 2.07: d3dbhg_
  • 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 2.07: d3dbhh1, d3dbhh2
  • 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 2.07: d3dbhi2, d3dbhi3
  • 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 2.07: d3dbhj_
  • 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 2.07: d3dbhk_
  • 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 2.07: d3dbhl_
  • Heterogens: ZN

PDB Chain Sequences:

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

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

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

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

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

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

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

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

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

    Sequence, based on observed residues (ATOM records): (download)
    >3dbhE (E:)
    kllkeqkydrqlrlwgdhgqealesahvclinatatgteilknlvlpgigsftiidgnqv
    sgedagnnfflqrssigknraeaameflqelnsdvsgsfveespenlldndpsffcrftv
    vvatqlpestslrladvlwnsqipllicrtyglvgymriiikehpvieshpdnaledlrl
    dkpfpelrehfqsydldhekkdhshtpwiviiakylaqwysetngripktykekedfrdl
    irqgilkpedeenfeeaiknvntalnttqipssiedifnddrcinitkqtpsfwilaral
    kefvakegqgnlpvrgtipdmiadsgkyiklqnvyrekakkdaaavgnhvakllqsigqa
    pesisekelkllcsnsaflrvvrcrslaeeygldtinkdeiissmdnpdneivlylmlra
    vdrfhkqqgrypgvsnyqveedigklkscltgflqeyglsvmvkddyvhefcrygaaeph
    tiaaflggaaaqevikiitkqfvifnntyiysgmsqtsatfql
    

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

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

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

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

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

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

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

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

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

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

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

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

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

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