3RK1 | pdb_00003rk1

'X-ray crystal Structure of the putative N-type ATP pyrophosphatase (PF0828) in complex with ATP from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target PfR23

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	d3rk1b1	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	N-type ATP pyrophosphatases	Putative N-type ATP pyrophosphatase PF0828	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
B	d3rk1b2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
A	d3rk1a_	Alpha and beta proteins (a/b)	Adenine nucleotide alpha hydrolase-like	Adenine nucleotide alpha hydrolases-like	N-type ATP pyrophosphatases	Putative N-type ATP pyrophosphatase PF0828	(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)
B	SCOP2B Superfamily	Adenine nucleotide alpha hydrolases-like	8040929	3001593	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Adenine nucleotide alpha hydrolases-like	8040929	3001593	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	Diphthami_syn_2	e3rk1B1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: Diphthami_syn_2	ECOD (1.6)
A	Diphthami_syn_2	e3rk1A1	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: Diphthami_syn_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B	3.90.1490.10	Alpha Beta	Alpha-Beta Complex	putative n-type atp pyrophosphatase, domain 2	putative n-type atp pyrophosphatase, domain 2	CATH (4.3.0)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
A	3.90.1490.10	Alpha Beta	Alpha-Beta Complex	putative n-type atp pyrophosphatase, domain 2	putative n-type atp pyrophosphatase, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01902	Diphthamide synthase (Diphthami_syn_2)	Diphthamide synthase	Diphthamide synthase catalyses the last amidation step of diphthamide biosynthesis using ammonium and ATP. Diphthamide synthase is evolutionarily conserved in eukaryotes. Diphthamide is a post-translationally modified histidine residue found on archa ...	Diphthamide synthase catalyses the last amidation step of diphthamide biosynthesis using ammonium and ATP. Diphthamide synthase is evolutionarily conserved in eukaryotes. Diphthamide is a post-translationally modified histidine residue found on archaeal and eukaryotic translation elongation factor 2 (eEF-2) [1]. In some members of this family e.g. Swiss:Q12429, this domain is associated with Pfam:PF01042. The enzyme classification is EC:6.3.1.14.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	N-type ATP pyrophosphatase superfamily	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 diphthine-ammonia ligase activity acid-ammonia (or amide) ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity	peptidyl-histidine modification macromolecule modification peptidyl-amino acid modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process protein histidyl modification to diphthamide	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR030662	Diphthine--ammonia ligase/Uncharacterised protein MJ0570	Family
A, B	IPR002761	Diphthamide synthase domain	Domain
A, B	IPR022427	Uncharacterised protein MJ0570, ATP-binding	Family
A, B	IPR005237	Uncharacterised protein MJ0570	Family
A, B	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	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.