2QKK | pdb_00002qkk

Human RNase H catalytic domain mutant D210N in complex with 14-mer RNA/DNA hybrid

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
W	SCOP2B Superfamily	Ribonuclease H-like	8075084	3000143	SCOP2B (2022-06-29)
V [auth S]	SCOP2B Superfamily	Ribonuclease H-like	8075084	3000143	SCOP2B (2022-06-29)
U [auth R]	SCOP2B Superfamily	Ribonuclease H-like	8075084	3000143	SCOP2B (2022-06-29)
T [auth N]	SCOP2B Superfamily	Ribonuclease H-like	8075084	3000143	SCOP2B (2022-06-29)
S [auth M]	SCOP2 Family	Ribonuclease H-like	8075083	4000541	SCOP2 (2022-06-29)
S [auth M]	SCOP2 Superfamily	Ribonuclease H-like	8075084	3000143	SCOP2 (2022-06-29)
R [auth J]	SCOP2B Superfamily	Ribonuclease H-like	8075084	3000143	SCOP2B (2022-06-29)
Q [auth I]	SCOP2B Superfamily	Ribonuclease H-like	8075084	3000143	SCOP2B (2022-06-29)
P [auth F]	SCOP2B Superfamily	Ribonuclease H-like	8075084	3000143	SCOP2B (2022-06-29)
O [auth E]	SCOP2B Superfamily	Ribonuclease H-like	8075084	3000143	SCOP2B (2022-06-29)
N [auth B]	SCOP2B Superfamily	Ribonuclease H-like	8075084	3000143	SCOP2B (2022-06-29)
M [auth A]	SCOP2B Superfamily	Ribonuclease H-like	8075084	3000143	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)
W	Pyr_redox_2	e2qkkW1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Pyr_redox_2	ECOD (v294.1)
V [auth S]	Pyr_redox_2	e2qkkS1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Pyr_redox_2	ECOD (v294.1)
U [auth R]	Pyr_redox_2	e2qkkR1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Pyr_redox_2	ECOD (v294.1)
T [auth N]	Pyr_redox_2	e2qkkN1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Pyr_redox_2	ECOD (v294.1)
S [auth M]	Pyr_redox_2	e2qkkM1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Pyr_redox_2	ECOD (v294.1)
R [auth J]	Pyr_redox_2	e2qkkJ1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Pyr_redox_2	ECOD (v294.1)
Q [auth I]	Pyr_redox_2	e2qkkI1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Pyr_redox_2	ECOD (v294.1)
P [auth F]	Pyr_redox_2	e2qkkF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Pyr_redox_2	ECOD (v294.1)
O [auth E]	Pyr_redox_2	e2qkkE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Pyr_redox_2	ECOD (v294.1)
N [auth B]	Pyr_redox_2	e2qkkB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Pyr_redox_2	ECOD (v294.1)
M [auth A]	Pyr_redox_2	e2qkkA1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Pyr_redox_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
W	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
V [auth S]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
U [auth R]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
T [auth N]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
S [auth M]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
R [auth J]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
Q [auth I]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
P [auth F]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
O [auth E]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
N [auth B]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
M [auth A]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], R [auth J], S [auth M], T [auth N], U [auth R], V [auth S], W	PF00075	RNase H (RNase_H)	RNase H	RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], R [auth J], S [auth M], T [auth N], U [auth R], V [auth S], W	Ribonuclease H1	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleic acid binding nuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleic acid binding nuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism RNA-DNA hybrid ribonuclease activity hydrolase activity hydrolase activity, acting on ester bonds RNA endonuclease activity RNA binding	catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process DNA replication, removal of RNA primer DNA metabolic process catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process DNA replication, removal of RNA primer DNA metabolic process DNA replication	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen
B [auth D], D [auth H], F [auth L], H [auth P], J [auth U], B [auth D], D [auth H], F [auth L], H [auth P], J [auth U], L [auth Z]	5'-D(GPGPAPAPTPCPAPGPGPTPGPTPCPG)-3'	-	-	-
A [auth C], C [auth G], E [auth K], G [auth O], I [auth T], A [auth C], C [auth G], E [auth K], G [auth O], I [auth T], K [auth X]	5'-R(CPGPAPCPAPCPCPUPGPAPUPUPCPC)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], R [auth J], S [auth M], T [auth N], U [auth R], V [auth S], W	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], R [auth J], S [auth M], T [auth N], U [auth R], V [auth S], W	IPR037056	Ribonuclease H1, N-terminal domain superfamily	Homologous Superfamily
M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], R [auth J], S [auth M], T [auth N], U [auth R], V [auth S], W	IPR002156	Ribonuclease H domain	Domain
M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], R [auth J], S [auth M], T [auth N], U [auth R], V [auth S], W	IPR050092	Ribonuclease H	Family
M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], R [auth J], S [auth M], T [auth N], U [auth R], V [auth S], W	IPR011320	Ribonuclease H1, N-terminal	Domain
M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], R [auth J], S [auth M], T [auth N], U [auth R], V [auth S], W	IPR009027	Large ribosomal subunit protein bL9/RNase H1, N-terminal	Homologous Superfamily
M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], R [auth J], S [auth M], T [auth N], U [auth R], V [auth S], W	IPR017067	Ribonuclease H1, eukaryote	Family
M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], R [auth J], S [auth M], T [auth N], U [auth R], V [auth S], W	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], M [auth A], N [auth B], O [auth E], P [auth F], Q [auth I], R [auth J], S [auth M], T [auth N], U [auth R], V [auth S], W	Pharos: O60930	progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 2 progressive external ophthalmoplegia adult-onset chronic progressive external ophthalmoplegia with mitochondrial myopathy muscle tissue disease osteosarcoma lung cancer muscular disease ovarian cancer psoriasis Mitochondrial Diseases myopathy

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.