6ZQH | pdb_00006zqh

Yeast Uba1 in complex with ubiquitin

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)
B	d6zqhb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d6zqhd_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	E2 binding domain-like	8003942	3000147	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8017546	3000112	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CC (catalytic cysteine) domain-like	8003552	3000140	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SCCH domain-like	8003543	3000139	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	FCCH domain-like	8003532	3000138	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003540	3000112	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8017546	3000112	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003540	3000112	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8017546	3000112	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	E2 binding domain-like	8003942	3000147	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SCCH domain-like	8003543	3000139	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CC (catalytic cysteine) domain-like	8003552	3000140	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003540	3000112	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	FCCH domain-like	8003532	3000138	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8017546	3000112	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Activating enzymes of the ubiquitin-like proteins	8003540	3000112	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	ubiquitin_1	e6zqhB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
D	ubiquitin_1	e6zqhD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
A	E1_FCCH	e6zqhA6	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: E1_FCCH	ECOD (1.6)
A	UBA_e1_thiolCys	e6zqhA5	A: alpha arrays	X: Catalytic cysteine domain in ubiquitin-activating enzyme (From Topology)	H: Catalytic cysteine domain in ubiquitin-activating enzyme (From Topology)	T: Catalytic cysteine domain in ubiquitin-activating enzyme	F: UBA_e1_thiolCys	ECOD (1.6)
A	ThiF_3	e6zqhA1	A: alpha arrays	X: Catalytic cysteine domain in ubiquitin-activating enzyme (From Topology)	H: Catalytic cysteine domain in ubiquitin-activating enzyme (From Topology)	T: Catalytic cysteine domain in ubiquitin-activating enzyme	F: ThiF_3	ECOD (1.6)
A	E1_UFD	e6zqhA4	A: a+b two layers	X: beta-Grasp	H: E2-binding domain of E1 (From Topology)	T: E2-binding domain of E1	F: E1_UFD	ECOD (1.6)
A	ThiF_1	e6zqhA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Activating enzymes of the ubiquitin-like proteins	F: ThiF_1	ECOD (1.6)
A	ThiF_3	e6zqhA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Activating enzymes of the ubiquitin-like proteins	F: ThiF_3	ECOD (1.6)
C	E1_FCCH	e6zqhC6	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: E1_FCCH	ECOD (1.6)
C	UBA_e1_thiolCys	e6zqhC2	A: alpha arrays	X: Catalytic cysteine domain in ubiquitin-activating enzyme (From Topology)	H: Catalytic cysteine domain in ubiquitin-activating enzyme (From Topology)	T: Catalytic cysteine domain in ubiquitin-activating enzyme	F: UBA_e1_thiolCys	ECOD (1.6)
C	ThiF_3	e6zqhC5	A: alpha arrays	X: Catalytic cysteine domain in ubiquitin-activating enzyme (From Topology)	H: Catalytic cysteine domain in ubiquitin-activating enzyme (From Topology)	T: Catalytic cysteine domain in ubiquitin-activating enzyme	F: ThiF_3	ECOD (1.6)
C	E1_UFD	e6zqhC3	A: a+b two layers	X: beta-Grasp	H: E2-binding domain of E1 (From Topology)	T: E2-binding domain of E1	F: E1_UFD	ECOD (1.6)
C	ThiF_1	e6zqhC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Activating enzymes of the ubiquitin-like proteins	F: ThiF_1	ECOD (1.6)
C	ThiF_3	e6zqhC4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Activating enzymes of the ubiquitin-like proteins	F: ThiF_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
A	2.40.30.180	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (utative)
A	3.10.290.60	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region	Chain A	CATH (utative)
C	2.40.30.180	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (utative)
C	3.10.290.60	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region	Chain A	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
A, C	PF00899	ThiF family (ThiF)	ThiF family	This domain is found in ubiquitin activating E1 family and members of the bacterial ThiF/MoeB/HesA family. It is repeated in Ubiquitin-activating enzyme E1 [1-3].	Domain
A, C	PF10585	Ubiquitin-activating enzyme, SCCH domain (UBA_E1_SCCH)	Ubiquitin-activating enzyme, SCCH domain	Ubiquitin-activating enzyme (E1 enzyme) activates ubiquitin by first adenylating with ATP its C-terminal glycine residue and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thiolester and free A ...	Ubiquitin-activating enzyme (E1 enzyme) activates ubiquitin by first adenylating with ATP its C-terminal glycine residue and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thiolester and free AMP. Later the ubiquitin moiety is transferred to a cysteine residue on one of the many forms of ubiquitin-conjugating enzymes (E2) [1]. This domain carries the last of five conserved cysteines that is part of the active site of the enzyme, responsible for ubiquitin thiolester complex formation, the active site being represented by the sequence motif PICTLKNFP [2,3,4]. The catalytic cysteine domain contains the E1 active site cysteine, and is divided in two half-domains, FCCH and SCCH, for 'first' and 'second' catalytic cysteine half-domain, respectively. This is the SCCH domain in which resides the catalytic cysteine [5].	Domain
A, C	PF09358	Ubiquitin fold domain (E1_UFD)	Ubiquitin fold domain	The ubiquitin fold domain is found at the C-terminus of ubiquitin-activating E1 family enzymes. This domain binds to E2 enzymes [1].	Domain
A, C	PF16190	Ubiquitin-activating enzyme E1 FCCH domain (E1_FCCH)	Ubiquitin-activating enzyme E1 FCCH domain	This domain is found in the ubiquitin-activating E1 family enzymes [1].	Domain
A, C	PF16191	Ubiquitin-activating enzyme E1 four-helix bundle (E1_4HB)	Ubiquitin-activating enzyme E1 four-helix bundle	This domain is found in the ubiquitin-activating E1 family enzymes [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Ubiquitin-40S ribosomal protein S31	protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding structural molecule activity protein tag activity molecular tag activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding structural molecule activity structural constituent of ribosome	primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process cytoplasmic translation metabolic process cellular process protein metabolic process macromolecule metabolic process ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process cytoplasmic translation metabolic process cellular process protein metabolic process macromolecule metabolic process ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process maturation of SSU-rRNA maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) cellular component organization or biogenesis RNA processing rRNA metabolic process nucleobase-containing compound biosynthetic process ribosomal small subunit biogenesis nucleic acid metabolic process catabolic process proteolysis involved in protein catabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis organelle assembly protein-containing complex organization membraneless organelle assembly ribosomal small subunit assembly protein-RNA complex assembly cellular component organization organelle organization protein-RNA complex organization cellular component assembly protein-containing complex assembly ribosome assembly maintenance of translational fidelity 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle
A, C	Ubiquitin-activating enzyme E1 1	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 ubiquitin-like modifier activating enzyme activity ligase activity, forming carbon-sulfur bonds catalytic activity, acting on a protein ubiquitin activating enzyme activity catalytic activity ligase activity ATP-dependent activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process macromolecule metabolic process protein metabolic process 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	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	IPR019954	Ubiquitin conserved site	Conserved Site
B, D	IPR000626	Ubiquitin-like domain	Domain
B, D	IPR038582	Small ribosomal subunit protein eS31 eukaryotic superfamily	Homologous Superfamily
B, D	IPR002906	Small ribosomal subunit protein eS31	Domain
B, D	IPR019956	Ubiquitin domain	Domain
B, D	IPR050158	Ubiquitin and ubiquitin-like	Family
B, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B, D	IPR011332	Zinc-binding ribosomal protein	Homologous Superfamily
A, C	IPR042302	Ubiquitin-activating enzyme E1, FCCH domain superfamily	Homologous Superfamily
A, C	IPR000011	Ubiquitin/SUMO-activating enzyme E1-like	Family
A, C	IPR045886	ThiF/MoeB/HesA family	Family
A, C	IPR042449	Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1	Homologous Superfamily
A, C	IPR019572	Ubiquitin-activating enzyme, SCCH domain	Domain
A, C	IPR042063	Ubiquitin-activating enzyme E1, SCCH domain	Homologous Superfamily
A, C	IPR000594	THIF-type NAD/FAD binding fold	Domain
A, C	IPR032420	Ubiquitin-activating enzyme E1, four-helix bundle	Domain
A, C	IPR018075	Ubiquitin-activating enzyme E1	Family
A, C	IPR032418	Ubiquitin-activating enzyme E1, FCCH domain	Domain
A, C	IPR018965	Ubiquitin-activating enzyme E1, C-terminal	Domain
A, C	IPR035985	Ubiquitin-activating enzyme-like	Homologous Superfamily
A, C	IPR033127	Ubiquitin-activating enzyme E1, Cys active site	Active Site
A, C	IPR038252	Ubiquitin-activating enzyme E1, C-terminal domain superfamily	Homologous Superfamily
A, C	IPR018074	Ubiquitin-activating enzyme E1, conserved site	Conserved Site