2ZV3 | pdb_00002zv3

Crystal structure of project MJ0051 from Methanocaldococcus jannaschii DSM 2661

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)
A	d2zv3a_	Alpha and beta proteins (a/b)	Peptidyl-tRNA hydrolase II	Peptidyl-tRNA hydrolase II	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
B	d2zv3b_	Alpha and beta proteins (a/b)	Peptidyl-tRNA hydrolase II	Peptidyl-tRNA hydrolase II	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
C	d2zv3c_	Alpha and beta proteins (a/b)	Peptidyl-tRNA hydrolase II	Peptidyl-tRNA hydrolase II	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
D	d2zv3d_	Alpha and beta proteins (a/b)	Peptidyl-tRNA hydrolase II	Peptidyl-tRNA hydrolase II	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
E	d2zv3e_	Alpha and beta proteins (a/b)	Peptidyl-tRNA hydrolase II	Peptidyl-tRNA hydrolase II	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
F	d2zv3f_	Alpha and beta proteins (a/b)	Peptidyl-tRNA hydrolase II	Peptidyl-tRNA hydrolase II	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
G	d2zv3g_	Alpha and beta proteins (a/b)	Peptidyl-tRNA hydrolase II	Peptidyl-tRNA hydrolase II	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
H	d2zv3h_	Alpha and beta proteins (a/b)	Peptidyl-tRNA hydrolase II	Peptidyl-tRNA hydrolase II	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
I	d2zv3i_	Alpha and beta proteins (a/b)	Peptidyl-tRNA hydrolase II	Peptidyl-tRNA hydrolase II	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	PTH2-like	8063647	4001109	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PTH2-like	8063648	3000791	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	PTH2-like	8063648	3000791	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PTH2-like	8063648	3000791	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PTH2-like	8063648	3000791	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PTH2-like	8063648	3000791	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	PTH2-like	8063648	3000791	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	PTH2-like	8063648	3000791	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	PTH2-like	8063648	3000791	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	PTH2-like	8063648	3000791	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	PTH2	e2zv3A1	A: a/b three-layered sandwiches	X: Peptidyl-tRNA hydrolase II (From Topology)	H: Peptidyl-tRNA hydrolase II (From Topology)	T: Peptidyl-tRNA hydrolase II	F: PTH2	ECOD (1.6)
B	PTH2	e2zv3B1	A: a/b three-layered sandwiches	X: Peptidyl-tRNA hydrolase II (From Topology)	H: Peptidyl-tRNA hydrolase II (From Topology)	T: Peptidyl-tRNA hydrolase II	F: PTH2	ECOD (1.6)
C	PTH2	e2zv3C1	A: a/b three-layered sandwiches	X: Peptidyl-tRNA hydrolase II (From Topology)	H: Peptidyl-tRNA hydrolase II (From Topology)	T: Peptidyl-tRNA hydrolase II	F: PTH2	ECOD (1.6)
D	PTH2	e2zv3D1	A: a/b three-layered sandwiches	X: Peptidyl-tRNA hydrolase II (From Topology)	H: Peptidyl-tRNA hydrolase II (From Topology)	T: Peptidyl-tRNA hydrolase II	F: PTH2	ECOD (1.6)
E	PTH2	e2zv3E1	A: a/b three-layered sandwiches	X: Peptidyl-tRNA hydrolase II (From Topology)	H: Peptidyl-tRNA hydrolase II (From Topology)	T: Peptidyl-tRNA hydrolase II	F: PTH2	ECOD (1.6)
F	PTH2	e2zv3F1	A: a/b three-layered sandwiches	X: Peptidyl-tRNA hydrolase II (From Topology)	H: Peptidyl-tRNA hydrolase II (From Topology)	T: Peptidyl-tRNA hydrolase II	F: PTH2	ECOD (1.6)
G	PTH2	e2zv3G1	A: a/b three-layered sandwiches	X: Peptidyl-tRNA hydrolase II (From Topology)	H: Peptidyl-tRNA hydrolase II (From Topology)	T: Peptidyl-tRNA hydrolase II	F: PTH2	ECOD (1.6)
H	PTH2	e2zv3H1	A: a/b three-layered sandwiches	X: Peptidyl-tRNA hydrolase II (From Topology)	H: Peptidyl-tRNA hydrolase II (From Topology)	T: Peptidyl-tRNA hydrolase II	F: PTH2	ECOD (1.6)
I	PTH2	e2zv3I1	A: a/b three-layered sandwiches	X: Peptidyl-tRNA hydrolase II (From Topology)	H: Peptidyl-tRNA hydrolase II (From Topology)	T: Peptidyl-tRNA hydrolase II	F: PTH2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1490.10	Alpha Beta	3-Layer(aba) Sandwich	Bit1	Bit1	CATH (4.3.0)
B	3.40.1490.10	Alpha Beta	3-Layer(aba) Sandwich	Bit1	Bit1	CATH (4.3.0)
C	3.40.1490.10	Alpha Beta	3-Layer(aba) Sandwich	Bit1	Bit1	CATH (4.3.0)
D	3.40.1490.10	Alpha Beta	3-Layer(aba) Sandwich	Bit1	Bit1	CATH (4.3.0)
E	3.40.1490.10	Alpha Beta	3-Layer(aba) Sandwich	Bit1	Bit1	CATH (4.3.0)
F	3.40.1490.10	Alpha Beta	3-Layer(aba) Sandwich	Bit1	Bit1	CATH (4.3.0)
G	3.40.1490.10	Alpha Beta	3-Layer(aba) Sandwich	Bit1	Bit1	CATH (4.3.0)
H	3.40.1490.10	Alpha Beta	3-Layer(aba) Sandwich	Bit1	Bit1	CATH (4.3.0)
I	3.40.1490.10	Alpha Beta	3-Layer(aba) Sandwich	Bit1	Bit1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I	PF01981	Peptidyl-tRNA hydrolase PTH2 (PTH2)	Peptidyl-tRNA hydrolase PTH2	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I	Peptidyl-tRNA hydrolase	hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid carboxylic ester hydrolase activity hydrolase activity catalytic activity, acting on a tRNA peptidyl-tRNA hydrolase activity catalytic activity	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression macromolecule biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR034759	Peptidyl-tRNA hydrolase, archaea	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR023476	Peptidyl-tRNA hydrolase II domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I	IPR002833	Peptidyl-tRNA hydrolase, PTH2	Family

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.