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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

3GZN

Structure of NEDD8-activating enzyme in complex with NEDD8 and MLN4924

Functional Information from GO Data
ChainGOidnamespacecontents
A0005515molecular_functionprotein binding
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0005886cellular_componentplasma membrane
A0006915biological_processapoptotic process
A0007165biological_processsignal transduction
A0008641molecular_functionubiquitin-like modifier activating enzyme activity
A0019781molecular_functionNEDD8 activating enzyme activity
A0031625molecular_functionubiquitin protein ligase binding
A0032991cellular_componentprotein-containing complex
A0033314biological_processmitotic DNA replication checkpoint signaling
A0042981biological_processregulation of apoptotic process
A0043523biological_processregulation of neuron apoptotic process
A0045116biological_processprotein neddylation
A0046982molecular_functionprotein heterodimerization activity
A0051402biological_processneuron apoptotic process
A0098978cellular_componentglutamatergic synapse
A0150052biological_processregulation of postsynapse assembly
B0000166molecular_functionnucleotide binding
B0005515molecular_functionprotein binding
B0005524molecular_functionATP binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0006508biological_processproteolysis
B0008641molecular_functionubiquitin-like modifier activating enzyme activity
B0016874molecular_functionligase activity
B0019781molecular_functionNEDD8 activating enzyme activity
B0019788molecular_functionNEDD8 transferase activity
B0032991cellular_componentprotein-containing complex
B0036211biological_processprotein modification process
B0042802molecular_functionidentical protein binding
B0043687biological_processpost-translational protein modification
B0045116biological_processprotein neddylation
B0046982molecular_functionprotein heterodimerization activity
C0005515molecular_functionprotein binding
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0005886cellular_componentplasma membrane
C0006915biological_processapoptotic process
C0007165biological_processsignal transduction
C0008641molecular_functionubiquitin-like modifier activating enzyme activity
C0019781molecular_functionNEDD8 activating enzyme activity
C0031625molecular_functionubiquitin protein ligase binding
C0032991cellular_componentprotein-containing complex
C0033314biological_processmitotic DNA replication checkpoint signaling
C0042981biological_processregulation of apoptotic process
C0043523biological_processregulation of neuron apoptotic process
C0045116biological_processprotein neddylation
C0046982molecular_functionprotein heterodimerization activity
C0051402biological_processneuron apoptotic process
C0098978cellular_componentglutamatergic synapse
C0150052biological_processregulation of postsynapse assembly
D0000166molecular_functionnucleotide binding
D0005515molecular_functionprotein binding
D0005524molecular_functionATP binding
D0005634cellular_componentnucleus
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0006508biological_processproteolysis
D0008641molecular_functionubiquitin-like modifier activating enzyme activity
D0016874molecular_functionligase activity
D0019781molecular_functionNEDD8 activating enzyme activity
D0019788molecular_functionNEDD8 transferase activity
D0032991cellular_componentprotein-containing complex
D0036211biological_processprotein modification process
D0042802molecular_functionidentical protein binding
D0043687biological_processpost-translational protein modification
D0045116biological_processprotein neddylation
D0046982molecular_functionprotein heterodimerization activity
I0005515molecular_functionprotein binding
I0005634cellular_componentnucleus
I0005654cellular_componentnucleoplasm
I0005737cellular_componentcytoplasm
I0005829cellular_componentcytosol
I0006508biological_processproteolysis
I0006511biological_processubiquitin-dependent protein catabolic process
I0009653biological_processanatomical structure morphogenesis
I0016567biological_processprotein ubiquitination
I0019941biological_processmodification-dependent protein catabolic process
I0030162biological_processregulation of proteolysis
I0031386molecular_functionprotein tag activity
I0031625molecular_functionubiquitin protein ligase binding
I0036211biological_processprotein modification process
I0045116biological_processprotein neddylation
I0070062cellular_componentextracellular exosome
I0072757biological_processcellular response to camptothecin
I0098794cellular_componentpostsynapse
I0098978cellular_componentglutamatergic synapse
I0150052biological_processregulation of postsynapse assembly
J0005515molecular_functionprotein binding
J0005634cellular_componentnucleus
J0005654cellular_componentnucleoplasm
J0005737cellular_componentcytoplasm
J0005829cellular_componentcytosol
J0006508biological_processproteolysis
J0006511biological_processubiquitin-dependent protein catabolic process
J0009653biological_processanatomical structure morphogenesis
J0016567biological_processprotein ubiquitination
J0019941biological_processmodification-dependent protein catabolic process
J0030162biological_processregulation of proteolysis
J0031386molecular_functionprotein tag activity
J0031625molecular_functionubiquitin protein ligase binding
J0036211biological_processprotein modification process
J0045116biological_processprotein neddylation
J0070062cellular_componentextracellular exosome
J0072757biological_processcellular response to camptothecin
J0098794cellular_componentpostsynapse
J0098978cellular_componentglutamatergic synapse
J0150052biological_processregulation of postsynapse assembly
Functional Information from PDB Data
site_idAC1
Number of Residues16
DetailsBINDING SITE FOR RESIDUE B39 J 464
ChainResidue
DGLY78
DILE148
DGLN149
DGLY165
DASP167
DALA171
DTRP174
JGLY76
DGLY79
DASP100
DMET101
DARG111
DGLN112
DLYS124
DASN146
DLYS147
site_idAC2
Number of Residues16
DetailsBINDING SITE FOR RESIDUE B39 I 464
ChainResidue
BGLY78
BGLY79
BASP100
BMET101
BASP102
BARG111
BGLN112
BLYS124
BASN146
BLYS147
BILE148
BGLN149
BASP167
BALA171
BTRP174
IGLY76
site_idAC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN B 465
ChainResidue
BCYS220
BCYS223
BCYS364
BCYS367
site_idAC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN D 465
ChainResidue
DCYS220
DCYS223
DCYS364
DCYS367
Functional Information from PROSITE/UniProt
site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KerVeEkegIPpqqQrLIYsGkqmnD
ChainResidueDetails
ILYS27-ASP52
site_idPS00865
Number of Residues9
DetailsUBIQUITIN_ACTIVAT_2 Ubiquitin-activating enzyme active site. PMCTIAsMP
ChainResidueDetails
BPRO235-PRO243
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues26
DetailsRegion: {"description":"Interaction with UBA3"}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues2
DetailsSite: {"description":"Interaction with UBA3"}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues2
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q8VBW6","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues106
DetailsRegion: {"description":"Interaction with UBE2M N-terminus"}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues14
DetailsRegion: {"description":"Interaction with NEDD8"}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues18
DetailsRegion: {"description":"Interaction with NAE1","evidences":[{"source":"PubMed","id":"12740388","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues2
DetailsActive site: {"description":"Glycyl thioester intermediate"}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues94
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues2
DetailsSite: {"description":"Determines specificity for NEDD8"}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues4
DetailsRegion: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues4
DetailsSite: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues2
DetailsModified residue: {"description":"(Microbial infection) Deamidated glutamine","evidences":[{"source":"PubMed","id":"20688984","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21903097","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23175788","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23589306","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26632597","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues2
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P29595","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)","evidences":[{"source":"PubMed","id":"38316879","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

247947

PDB entries from 2026-01-21

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