4X57 | pdb_00004x57

Structure of an Arabidopsis E2 / Membrane-anchored Ubiquitin-fold Protein Complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d4x57d_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d4x57b_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d4x57c1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	automated matches	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d4x57c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d4x57a1	Alpha and beta proteins (a+b)	UBC-like	UBC-like	automated matches	automated matches	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d4x57a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse-ear cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2 Family	Ubiquitin-related	8088982	4000962	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Ubiquitin-like	8088983	3000157	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8088983	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	UBC-like	8059974	3000570	SCOP2B (2022-06-29)
A	SCOP2 Family	UBC-related	8059973	4001046	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	UBC-like	8059974	3000570	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Oxidored_q6	e4x57D1	A: a/b three-layered sandwiches	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Oxidored_q6	ECOD (v294.1)
B	Oxidored_q6	e4x57B1	A: a/b three-layered sandwiches	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Oxidored_q6	ECOD (v294.1)
C	Oxidored_q6	e4x57C1	A: a/b three-layered sandwiches	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Oxidored_q6	ECOD (v294.1)
A	Oxidored_q6	e4x57A1	A: a/b three-layered sandwiches	X: ACP-like	H: Acyl-carrier protein (ACP)	T: Acyl-carrier protein (ACP)	F: Oxidored_q6	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)
A	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF13881	Ubiquitin-2 like Rad60 SUMO-like (Rad60-SLD_2)	Ubiquitin-2 like Rad60 SUMO-like		Domain
A, C	PF00179	Ubiquitin-conjugating enzyme (UQ_con)	Ubiquitin-conjugating enzyme	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cystein ...	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Membrane-anchored ubiquitin-fold protein 3	-	-	cell periphery cellular anatomical structure plasma membrane membrane
A, C	Ubiquitin-conjugating enzyme E2 8	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin conjugating enzyme activity ubiquitin-like protein conjugating enzyme activity	catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein polyubiquitination protein ubiquitination macromolecule modification catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process protein polyubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal developmental process multicellular organismal process reproductive system development endosperm development reproductive process developmental process involved in reproduction tissue development multicellular organism development fruit development seed development anatomical structure development reproductive structure development post-embryonic development system development	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR017000	Membrane-anchored ubiquitin-fold protein	Family
B, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B, D	IPR000626	Ubiquitin-like domain	Domain
B, D	IPR039540	UBL3-like, ubiquitin domain	Domain
B, D	IPR040015	UBL3-like	Family
A, C	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
A, C	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
A, C	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.