4IDI | pdb_00004idi

Crystal Structure of Rurm1-related protein from Plasmodium Yoelii, PY06420

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	d4idid_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	MoaD/ThiS	automated matches	automated matches	(Plasmodium yoelii yoelii ) [TaxId: 73239 ],	SCOPe (2.08)
C	d4idic_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	MoaD/ThiS	automated matches	automated matches	(Plasmodium yoelii yoelii ) [TaxId: 73239 ],	SCOPe (2.08)
B	d4idib_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	MoaD/ThiS	automated matches	automated matches	(Plasmodium yoelii yoelii ) [TaxId: 73239 ],	SCOPe (2.08)
A	d4idia_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	MoaD/ThiS	automated matches	automated matches	(Plasmodium yoelii yoelii ) [TaxId: 73239 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	MoaD/ThiS-like	8088560	3000330	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MoaD/ThiS-like	8088560	3000330	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MoaD/ThiS-like	8088560	3000330	SCOP2B (2022-06-29)
A	SCOP2 Family	C9orf74 homolog	8088559	4003667	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	MoaD/ThiS-like	8088560	3000330	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	Peptidase_M49	e4idiD3	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (v294.1)
C	Peptidase_M49	e4idiC3	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (v294.1)
B	Peptidase_M49	e4idiB3	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (v294.1)
A	YchF-GTPase_C	e4idiA2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: YchF-GTPase_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
C	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
B	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)
A	3.10.20.30	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Beta-grasp domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF09138	Urm1 (Ubiquitin related modifier) (Urm1)	Urm1 (Ubiquitin related modifier)	Urm1 is a ubiquitin related protein that modifies proteins in the yeast ubiquitin-like pathway urmylation [1]. Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and ...	Urm1 is a ubiquitin related protein that modifies proteins in the yeast ubiquitin-like pathway urmylation [1]. Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and sequence features of the common ancestor of the entire superfamily [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Oryza sativa Rurm1-related	-	primary metabolic process protein urmylation macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal tRNA thio-modification tRNA modification RNA metabolic process primary metabolic process protein urmylation macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal tRNA thio-modification tRNA modification RNA metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing RNA processing tRNA wobble uridine modification tRNA wobble base modification	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR015221	Ubiquitin-related modifier 1	Family
A, B, C, D	IPR016155	Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp	Homologous Superfamily
A, B, C, D	IPR012675	Beta-grasp domain superfamily	Homologous Superfamily

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.