eF-site ID 2nvu-ABCIJ
PDB Code 2nvu
Chain A, B, C, I, J

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Title Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like protein activation complex
Classification PROTEIN TURNOVER, LIGASE
Compound NEDD8-activating enzyme E1 regulatory subunit
Source Homo sapiens (Human) (NEDD8_HUMAN)
Sequence A:  GKLLKEQKYDRQLRLWGDHGQEALESAHVCLINATATGTE
ILKNLVLPGIGSFTIIDGNQVSGEDAGNNFFLQRSSIGKN
RAEAAMEFLQELNSDVSGSFVEESPENLLDNDPSFFCRFT
VVVATQLPESTSLRLADVLWNSQIPLLICRTYGLVGYMRI
IIKEHPVIESHPDNALEDLRLDKPFPELREHFQSYDLDHM
EKKDHSHTPWIVIIAKYLAQWYSETNGRIPKTYKEKEDFR
DLIRQGILKNENGAPEDEENFEEAIKNVNTALNTTQIPSS
IEDIFNDDRCINITKQTPSFWILARALKEFVAKEGQGNLP
VRGTIPDMIADSGKYIKLQNVYREKAKKDAAAVGNHVAKL
LQSIGQAPESISEKELKLLCSNSAFLRVVRCRSLAEEYGL
DTINKDEIISSMDNPDNEIVLYLMLRAVDRFHKQQGRYPG
VSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDYVHEFCR
YGAAEPHTIAAFLGGAAAQEVIKIITKQFVIFNNTYIYSG
MSQTSATFQL
B:  KIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHP
DKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEIT
PDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKD
LLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPL
IAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIK
NKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKV
NYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFL
ENYLLTDEGLEAVNKDKVALKSYEEEATMENAQKGEIMPN
IPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAADW
EGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLV
IGAGGLGCELLKNLALSGFRQIHVIDMDTIDVSNLNRQFL
FRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNKIQDFNDT
FYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSS
IVPLIDGGTEGFKGNARVILPGMTACIECTLELYPPQVNF
PMCTIASMPRLPEHCIEYVRMLQWPKEQPFGEGVPLDGDD
PEHIQWIFQKSLERASQYNIRGVTYRLTQGVVKRIIPAVA
STNAVIAAVCATEVFKIATSAYIPLNNYLVFNDVDGLYTY
TFEAERKENCPACSQLPQNIQFSPSAKLQEVLDYLTNSAS
LQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLK
ELGLVDGQELAVADVTTPQTVLFKLHFTS
C:  KLFSLKQQKKEEEKGSSKKASAAQLRIQKDINELNLPKTC
DISFSDPDDLLNFKLVICPDEGFYKSGKFVFSFKVGQGYP
HDPPKVKCETMVYHPNIDLEGNVALNILREDWKPVLTINS
IIYGLQYLFLEPNPEDPLNKEAAEVLQNNRRLFEQNVQRS
MRGGYIGSTYFERCLK
I:  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQ
QRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG
J:  MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQ
QRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG
Description


Functional site

1) chain B
residue 2146
type
sequence D
description BINDING SITE FOR RESIDUE MG B 101
source : AC1

2) chain B
residue 2199
type
sequence C
description BINDING SITE FOR RESIDUE ZN B 102
source : AC2

3) chain B
residue 2202
type
sequence C
description BINDING SITE FOR RESIDUE ZN B 102
source : AC2

4) chain B
residue 2343
type
sequence C
description BINDING SITE FOR RESIDUE ZN B 102
source : AC2

5) chain B
residue 2346
type
sequence C
description BINDING SITE FOR RESIDUE ZN B 102
source : AC2

6) chain A
residue 15
type
sequence R
description BINDING SITE FOR RESIDUE ATP B 103
source : AC3

7) chain B
residue 2056
type
sequence A
description BINDING SITE FOR RESIDUE ATP B 103
source : AC3

8) chain B
residue 2057
type
sequence G
description BINDING SITE FOR RESIDUE ATP B 103
source : AC3

9) chain B
residue 2079
type
sequence D
description BINDING SITE FOR RESIDUE ATP B 103
source : AC3

10) chain B
residue 2080
type
sequence M
description BINDING SITE FOR RESIDUE ATP B 103
source : AC3

11) chain B
residue 2081
type
sequence D
description BINDING SITE FOR RESIDUE ATP B 103
source : AC3

12) chain B
residue 2087
type
sequence N
description BINDING SITE FOR RESIDUE ATP B 103
source : AC3

13) chain B
residue 2090
type
sequence R
description BINDING SITE FOR RESIDUE ATP B 103
source : AC3

14) chain B
residue 2091
type
sequence Q
description BINDING SITE FOR RESIDUE ATP B 103
source : AC3

15) chain B
residue 2103
type
sequence K
description BINDING SITE FOR RESIDUE ATP B 103
source : AC3

16) chain B
residue 2125
type
sequence N
description BINDING SITE FOR RESIDUE ATP B 103
source : AC3

17) chain B
residue 2126
type
sequence K
description BINDING SITE FOR RESIDUE ATP B 103
source : AC3

18) chain B
residue 2127
type
sequence I
description BINDING SITE FOR RESIDUE ATP B 103
source : AC3

19) chain B
residue 2128
type
sequence Q
description BINDING SITE FOR RESIDUE ATP B 103
source : AC3

20) chain B
residue 2144
type
sequence G
description BINDING SITE FOR RESIDUE ATP B 103
source : AC3

21) chain B
residue 2146
type
sequence D
description BINDING SITE FOR RESIDUE ATP B 103
source : AC3

22) chain I
residue 76
type
sequence G
description BINDING SITE FOR RESIDUE ATP B 103
source : AC3

23) chain I
residue 27-52
type prosite
sequence KERVEEKEGIPPQQQRLIYSGKQMND
description UBIQUITIN_1 Ubiquitin domain signature. KerVeEkegIPpqqQrLIYsGkqmnD
source prosite : PS00299

24) chain B
residue 2214-2222
type prosite
sequence PMCTIASMP
description UBIQUITIN_ACTIVAT_2 Ubiquitin-activating enzyme active site. PMCTIAsMP
source prosite : PS00865

25) chain B
residue 1108-1125
type prosite
sequence PIAVEALSLIYNKDLLPN
description SBP_BACTERIAL_1 Bacterial extracellular solute-binding proteins, family 1 signature. PIAvEalSLIYNkdlLpN
source prosite : PS01037

26) chain I
residue 8
type SITE
sequence L
description Interaction with UBE1C => ECO:0000269|PubMed:14690597
source Swiss-Prot : SWS_FT_FI1

27) chain I
residue 44
type SITE
sequence I
description Interaction with UBE1C => ECO:0000269|PubMed:14690597
source Swiss-Prot : SWS_FT_FI1

28) chain J
residue 8
type SITE
sequence L
description Interaction with UBE1C => ECO:0000269|PubMed:14690597
source Swiss-Prot : SWS_FT_FI1

29) chain J
residue 44
type SITE
sequence I
description Interaction with UBE1C => ECO:0000269|PubMed:14690597
source Swiss-Prot : SWS_FT_FI1

30) chain I
residue 40
type MOD_RES
sequence Q
description (Microbial infection) Deamidated glutamine => ECO:0000269|PubMed:20688984, ECO:0000269|PubMed:21903097, ECO:0000269|PubMed:23175788, ECO:0000269|PubMed:23589306, ECO:0000269|PubMed:26632597
source Swiss-Prot : SWS_FT_FI2

31) chain J
residue 40
type MOD_RES
sequence Q
description (Microbial infection) Deamidated glutamine => ECO:0000269|PubMed:20688984, ECO:0000269|PubMed:21903097, ECO:0000269|PubMed:23175788, ECO:0000269|PubMed:23589306, ECO:0000269|PubMed:26632597
source Swiss-Prot : SWS_FT_FI2

32) chain I
residue 48
type MOD_RES
sequence K
description N6-acetyllysine => ECO:0000250|UniProtKB:P29595
source Swiss-Prot : SWS_FT_FI3

33) chain J
residue 48
type MOD_RES
sequence K
description N6-acetyllysine => ECO:0000250|UniProtKB:P29595
source Swiss-Prot : SWS_FT_FI3

34) chain I
residue 76
type CROSSLNK
sequence G
description Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
source Swiss-Prot : SWS_FT_FI4

35) chain J
residue 76
type CROSSLNK
sequence G
description Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
source Swiss-Prot : SWS_FT_FI4

36) chain C
residue 174
type MOD_RES
sequence G
description Omega-N-methylarginine; alternate => ECO:0007744|PubMed:24129315
source Swiss-Prot : SWS_FT_FI5


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