Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2NVU

Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like protein activation complex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005515	molecular_function	protein binding
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0005886	cellular_component	plasma membrane
A	0006915	biological_process	apoptotic process
A	0007165	biological_process	signal transduction
A	0008641	molecular_function	ubiquitin-like modifier activating enzyme activity
A	0019781	molecular_function	NEDD8 activating enzyme activity
A	0031625	molecular_function	ubiquitin protein ligase binding
A	0032991	cellular_component	protein-containing complex
A	0033314	biological_process	mitotic DNA replication checkpoint signaling
A	0042981	biological_process	regulation of apoptotic process
A	0043523	biological_process	regulation of neuron apoptotic process
A	0045116	biological_process	protein neddylation
A	0046982	molecular_function	protein heterodimerization activity
A	0051402	biological_process	neuron apoptotic process
A	0098978	cellular_component	glutamatergic synapse
A	0150052	biological_process	regulation of postsynapse assembly
B	0008641	molecular_function	ubiquitin-like modifier activating enzyme activity
B	0008643	biological_process	carbohydrate transport
B	0015144	molecular_function	carbohydrate transmembrane transporter activity
B	0019781	molecular_function	NEDD8 activating enzyme activity
B	0045116	biological_process	protein neddylation
B	0055085	biological_process	transmembrane transport
C	0000166	molecular_function	nucleotide binding
C	0004842	molecular_function	ubiquitin-protein transferase activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005730	cellular_component	nucleolus
C	0005829	cellular_component	cytosol
C	0016604	cellular_component	nuclear body
C	0016740	molecular_function	transferase activity
C	0019787	molecular_function	ubiquitin-like protein transferase activity
C	0019788	molecular_function	NEDD8 transferase activity
C	0032446	biological_process	protein modification by small protein conjugation
C	0036211	biological_process	protein modification process
C	0043687	biological_process	post-translational protein modification
C	0045116	biological_process	protein neddylation
C	0061654	molecular_function	NEDD8 conjugating enzyme activity
C	0098793	cellular_component	presynapse
C	0098794	cellular_component	postsynapse
C	0098978	cellular_component	glutamatergic synapse
C	0150052	biological_process	regulation of postsynapse assembly
I	0005515	molecular_function	protein binding
I	0005634	cellular_component	nucleus
I	0005654	cellular_component	nucleoplasm
I	0005737	cellular_component	cytoplasm
I	0005829	cellular_component	cytosol
I	0006508	biological_process	proteolysis
I	0006511	biological_process	ubiquitin-dependent protein catabolic process
I	0009653	biological_process	anatomical structure morphogenesis
I	0016567	biological_process	protein ubiquitination
I	0019941	biological_process	modification-dependent protein catabolic process
I	0030162	biological_process	regulation of proteolysis
I	0031386	molecular_function	protein tag activity
I	0031625	molecular_function	ubiquitin protein ligase binding
I	0036211	biological_process	protein modification process
I	0045116	biological_process	protein neddylation
I	0070062	cellular_component	extracellular exosome
I	0072757	biological_process	cellular response to camptothecin
I	0098794	cellular_component	postsynapse
I	0098978	cellular_component	glutamatergic synapse
I	0150052	biological_process	regulation of postsynapse assembly
J	0005515	molecular_function	protein binding
J	0005634	cellular_component	nucleus
J	0005654	cellular_component	nucleoplasm
J	0005737	cellular_component	cytoplasm
J	0005829	cellular_component	cytosol
J	0006508	biological_process	proteolysis
J	0006511	biological_process	ubiquitin-dependent protein catabolic process
J	0009653	biological_process	anatomical structure morphogenesis
J	0016567	biological_process	protein ubiquitination
J	0019941	biological_process	modification-dependent protein catabolic process
J	0030162	biological_process	regulation of proteolysis
J	0031386	molecular_function	protein tag activity
J	0031625	molecular_function	ubiquitin protein ligase binding
J	0036211	biological_process	protein modification process
J	0045116	biological_process	protein neddylation
J	0070062	cellular_component	extracellular exosome
J	0072757	biological_process	cellular response to camptothecin
J	0098794	cellular_component	postsynapse
J	0098978	cellular_component	glutamatergic synapse
J	0150052	biological_process	regulation of postsynapse assembly

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG B 101

Chain	Residue
B	HOH45
B	ATP103
B	ASP2146

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 102

Chain	Residue
B	CYS2199
B	CYS2202
B	CYS2343
B	CYS2346

site_id	AC3
Number of Residues	22
Details	BINDING SITE FOR RESIDUE ATP B 103

Chain	Residue
B	HOH31
B	HOH40
B	HOH45
B	MG101
B	ALA2056
B	GLY2057
B	ASP2079
B	MET2080
B	ASP2081
B	ASN2087
B	ARG2090
B	GLN2091
B	LYS2103
B	ASN2125
B	LYS2126
B	ILE2127
B	GLN2128
B	GLY2144
B	ASP2146
I	GLY76
A	ARG15
B	HOH5

Functional Information from PROSITE/UniProt

site_id	PS00299
Number of Residues	26
Details	UBIQUITIN_1 Ubiquitin domain signature. KerVeEkegIPpqqQrLIYsGkqmnD

Chain	Residue	Details
I	LYS27-ASP52

site_id	PS00865
Number of Residues	9
Details	UBIQUITIN_ACTIVAT_2 Ubiquitin-activating enzyme active site. PMCTIAsMP

Chain	Residue	Details
B	PRO2214-PRO2222

site_id	PS01037
Number of Residues	18
Details	SBP_BACTERIAL_1 Bacterial extracellular solute-binding proteins, family 1 signature. PIAvEalSLIYNkdlLpN

Chain	Residue	Details
B	PRO1108-ASN1125

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	13
Details	Region: {"description":"Interaction with UBA3"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	1
Details	Site: {"description":"Interaction with UBA3"}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q8VBW6","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	53
Details	Region: {"description":"Interaction with UBE2M N-terminus"}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	7
Details	Region: {"description":"Interaction with NEDD8"}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	9
Details	Region: {"description":"Interaction with NAE1","evidences":[{"source":"PubMed","id":"12740388","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	95
Details	Region: {"description":"Interaction with UBE2M core domain"}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	1
Details	Active site: {"description":"Glycyl thioester intermediate"}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	47
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	1
Details	Site: {"description":"Determines specificity for NEDD8"}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	144
Details	Domain: {"description":"UBC core","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	1
Details	Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	1
Details	Modified residue: {"description":"Omega-N-methylarginine; alternate","evidences":[{"source":"PubMed","id":"24129315","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	4
Details	Region: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	4
Details	Site: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	2
Details	Modified 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"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P29595","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)","evidences":[{"source":"PubMed","id":"38316879","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)