1KHW | pdb_00001khw

Crystal Structure of Rabbit Hemorrhagic Disease Virus RNA-dependent RNA polymerase complexed with Mn2+

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	d1khwb_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	RNA-dependent RNA-polymerase	Viral RNA polymerase	(Rabbit hemorrhagic disease virus ) [TaxId: 11976 ],	SCOPe (2.08)
A	d1khwa_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	RNA-dependent RNA-polymerase	Viral RNA polymerase	(Rabbit hemorrhagic disease virus ) [TaxId: 11976 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8038256	3001272	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8038256	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8038256	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8038256	3001272	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	TFR_dimer	e1khwB1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: TFR_dimer	ECOD (develop294)
B	RNase_P_Rpp14	e1khwB2	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)
A	TFR_dimer	e1khwA1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F: TFR_dimer	ECOD (develop294)
A	RNase_P_Rpp14	e1khwA2	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	4.10.8.20	Few Secondary Structures	Irregular	Luciferase	domain 5	CATH (4.3.0)
B	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
B	6.10.140.320	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
B	1.20.960.20	Mainly Alpha	Up-down Bundle	Mitochondrial Import Receptor Subunit Tom20	Chain A	CATH (4.3.0)
A	4.10.8.20	Few Secondary Structures	Irregular	Luciferase	domain 5	CATH (4.3.0)
A	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
A	6.10.140.320	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
A	1.20.960.20	Mainly Alpha	Up-down Bundle	Mitochondrial Import Receptor Subunit Tom20	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00680	Viral RNA-dependent RNA polymerase (RdRP_1)	Viral RNA-dependent RNA polymerase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	RNA-DIRECTED RNA POLYMERASE	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups RNA binding binding nucleic acid 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 pyrophosphatase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides nucleic acid conformation isomerase activity isomerase activity helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity ATP-dependent activity	RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process gene expression DNA-templated transcription proteolysis protein metabolic process	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region viral capsid virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
A, B	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B	IPR014759	Helicase, superfamily 3, single-stranded RNA virus	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR000317	Peptidase C24, Calicivirus polyprotein Orf1	Domain
A, B	IPR049434	VPg	Family
A, B	IPR029053	Viral coat protein subunit	Homologous Superfamily
A, B	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B	IPR004005	Calicivirus coat protein	Domain
A, B	IPR004004	Helicase/polymerase/peptidase polyprotein, Calicivirus-type	Family
A, B	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B	IPR033703	Picornavirus/Calicivirus coat protein	Domain
A, B	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
A, B	IPR000605	Helicase, superfamily 3, single-stranded DNA/RNA virus	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.