5LDA | pdb_00005lda

Structure of deubiquitinating enzyme homolog (Pyrococcus furiosus JAMM1) in complex with ubiquitin-like SAMP2.

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	d5ldab_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	MoaD/ThiS	ThiS	Hypothetical protein PF1061	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	JAB1/MPN domain-like	8053297	3001105	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MoaD/ThiS-like	8041050	3000330	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)
A		e5ldaA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Immunoglobulin-related	T: HAD-like	F:	ECOD (v294.1)
B		e5ldaB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Immunoglobulin-related	T: HAD-like	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	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	PF14464	Prokaryotic homologs of the JAB domain (Prok-JAB)	Prokaryotic homologs of the JAB domain	-	Family
B	PF02597	ThiS family (ThiS)	ThiS family	ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer Swiss:O32583. ThiS is coded in the thiCEFSGH operon in E. coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the a ...	ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer Swiss:O32583. ThiS is coded in the thiCEFSGH operon in E. coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS [1]. MoaD, Swiss:P30748 a protein involved sulphur transfer in molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	JAMM1	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein hydrolase activity metallopeptidase activity exopeptidase activity catalytic activity metalloexopeptidase activity	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	-
B	SAMP2	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR028090	JAB domain, prokaryotic	Domain
A	IPR037518	MPN domain	Domain
A	IPR051929	Viral Assembly and Modifier Protease	Family
A	IPR000555	JAB1/MPN/MOV34 metalloenzyme domain	Domain
B	IPR003749	Sulfur carrier ThiS/MoaD-like	Family
B	IPR016155	Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp	Homologous Superfamily
B	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.