1CKM | pdb_00001ckm

STRUCTURE OF TWO DIFFERENT CONFORMATIONS OF MRNA CAPPING ENZYME IN COMPLEX WITH GTP

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	d1ckmb1	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA ligase/mRNA capping enzyme postcatalytic domain	RNA guanylyltransferase (mRNA capping enzyme)	(Paramecium bursaria Chlorella virus 1 ) [TaxId: 10506 ],	SCOPe (2.08)
B	d1ckmb2	Alpha and beta proteins (a+b)	ATP-grasp	DNA ligase/mRNA capping enzyme, catalytic domain	mRNA capping enzyme	RNA guanylyltransferase (mRNA capping enzyme), N-terminal domain	(Paramecium bursaria Chlorella virus 1 ) [TaxId: 10506 ],	SCOPe (2.08)
A	d1ckma1	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA ligase/mRNA capping enzyme postcatalytic domain	RNA guanylyltransferase (mRNA capping enzyme)	(Paramecium bursaria Chlorella virus 1 ) [TaxId: 10506 ],	SCOPe (2.08)
A	d1ckma2	Alpha and beta proteins (a+b)	ATP-grasp	DNA ligase/mRNA capping enzyme, catalytic domain	mRNA capping enzyme	RNA guanylyltransferase (mRNA capping enzyme), N-terminal domain	(Paramecium bursaria Chlorella virus 1 ) [TaxId: 10506 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8041957	3000135	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8036593	3000798	SCOP2B (2022-06-29)
A	SCOP2 Family	mRNA capping enzyme guanylyltransferase domain-like	8024214	4002077	SCOP2 (2022-06-29)
A	SCOP2 Family	DNA ligase/mRNA capping enzyme postcatalytic domain-like	8029578	4001931	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8036593	3000798	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleic acid-binding proteins	8041957	3000135	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	Stap_Strp_toxin	e1ckmB1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Stap_Strp_toxin	ECOD (develop294)
B	LRR_6,LRR_RI_capping	e1ckmB2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: LRR_6,LRR_RI_capping	ECOD (develop294)
A	mRNA_cap_C	e1ckmA1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: mRNA_cap_C	ECOD (develop294)
A	mRNA_cap_enzyme	e1ckmA2	A: beta duplicates or obligate multimers	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: mRNA_cap_enzyme	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
B	4.10.87.10	Few Secondary Structures	Irregular	mRNA Capping Enzyme	Chain	CATH (4.3.0)
A	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
A	4.10.87.10	Few Secondary Structures	Irregular	mRNA Capping Enzyme	Chain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03919	mRNA capping enzyme, C-terminal domain (mRNA_cap_C)	mRNA capping enzyme, C-terminal domain		Domain
A, B	PF01331	mRNA capping enzyme, catalytic domain (mRNA_cap_enzyme)	mRNA capping enzyme, catalytic domain	This family represents the ATP binding catalytic domain of the mRNA capping enzyme.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	MRNA CAPPING ENZYME	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 guanylyltransferase activity mRNA guanylyltransferase activity RNA guanylyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid transferase activity catalytic activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups guanyl nucleotide binding GTP binding guanyl ribonucleotide binding	7-methylguanosine mRNA capping RNA metabolic process primary metabolic process 7-methylguanosine RNA capping RNA capping gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process 7-methylguanosine mRNA capping RNA metabolic process primary metabolic process 7-methylguanosine RNA capping RNA capping gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 5'-end processing metabolic process cellular process RNA processing macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001339	mRNA capping enzyme, adenylation domain	Domain
A, B	IPR051029	mRNA_Capping_Enz/RNA_Phosphat	Unknown
A, B	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, B	IPR013846	mRNA capping enzyme, C-terminal domain	Domain

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.