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 2.03 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 2.03: 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 2.03: d3dbhb_
  • 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: 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 2.03: d3dbhd_
  • 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: 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 2.03: d3dbhf_
  • 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: 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 2.03: d3dbhh_
  • 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: d3dbhi_
  • 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: 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 2.03: 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 2.03: 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