2PHN | pdb_00002phn

Crystal structure of an amide bond forming F420-gamma glutamyl ligase from Archaeoglobus fulgidus

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	d2phnb_	Alpha and beta proteins (a+b)	CofE-like	CofE-like	CofE-like	F420-0:gamma-glutamyl ligase CofE	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)
A	d2phna_	Alpha and beta proteins (a+b)	CofE-like	CofE-like	CofE-like	F420-0:gamma-glutamyl ligase CofE	(Archaeoglobus fulgidus DSM 4304 ) [TaxId: 224325 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	CofE-like	8043883	3000257	SCOP2B (2022-06-29)
A	SCOP2 Family	CofE-like	8031505	4000423	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	CofE-like	8043883	3000257	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)
B	HHH_5	e2phnB1	A: alpha bundles	X: EGF-like	H: YozE-like	T: YozE-like	F: HHH_5	ECOD (develop294)
B	tRNA-synt_2	e2phnB2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: tRNA-synt_2	ECOD (develop294)
A	F420_ligase	e2phnA1	A: alpha arrays	X: HTH	H: CofE insertion domain	T: CofE insertion domain	F: F420_ligase	ECOD (develop294)
A	F420_ligase	e2phnA2	A: a+b three layers	X: CofE-like	H: CofE-like	T: CofE-like	F: F420_ligase	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.1330.100	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
B	3.90.1660.10	Alpha Beta	Alpha-Beta Complex	CofE-like fold	CofE-like domain	CATH (4.3.0)
A	3.30.1330.100	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
A	3.90.1660.10	Alpha Beta	Alpha-Beta Complex	CofE-like fold	CofE-like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01996	F420-0:Gamma-glutamyl ligase (F420_ligase)	F420-0:Gamma-glutamyl ligase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	F420-0:gamma-glutamyl ligase	acid-amino acid ligase activity coenzyme F420-0 gamma-glutamyl ligase activity coenzyme F420-1:gamma-L-glutamate ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity coenzyme F420-0:L-glutamate ligase activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding acid-amino acid ligase activity coenzyme F420-0 gamma-glutamyl ligase activity coenzyme F420-1:gamma-L-glutamate ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity coenzyme F420-0:L-glutamate ligase activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding metal ion binding	oxoacid metabolic process carboxylic acid metabolic process carbohydrate derivative metabolic process organic acid metabolic process organophosphate metabolic process F420-0 metabolic process phosphate-containing compound metabolic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process alditol phosphate metabolic process phosphorus metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002847	Coenzyme F420:L-glutamate ligase-like domain	Domain
A, B	IPR023659	Coenzyme F420:L-glutamate ligase, archaeal	Family
A, B	IPR008225	Coenzyme F420:L-glutamate ligase	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.