5GQ9 | pdb_00005gq9

Crystal structure of Thermus thermophilus Argonaute in complex with g1C siDNA and DNA target

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth B]	SCOP2B Superfamily	Mid domain of argonaute	8053636	3002210	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	RNA-binding domain, RBD	8053634	3000110	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Ribonuclease H-like	8053637	3000143	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	PAZ domain	8053635	3001750	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Mid domain of argonaute	8053636	3002210	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8053637	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RNA-binding domain, RBD	8053634	3000110	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)
D [auth B]	EUF07576	e5gq9B2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: EUF07576	ECOD (1.6)
D [auth B]	EUF08364	e5gq9B1	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: EUF08364	ECOD (1.6)
D [auth B]	EUF08368	e5gq9B4	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: EUF08368	ECOD (1.6)
D [auth B]	Piwi_piwi-like_ProArk	e5gq9B5	A: a/b three-layered sandwiches	X: Middle domain in Argonaute homologs (From Topology)	H: Middle domain in Argonaute homologs (From Topology)	T: Middle domain in Argonaute homologs	F: Piwi_piwi-like_ProArk	ECOD (1.6)
D [auth B]	Piwi_C_1	e5gq9B3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Piwi_C_1	ECOD (1.6)
A	EUF07576	e5gq9A1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: EUF07576	ECOD (1.6)
A	EUF08364	e5gq9A5	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: EUF08364	ECOD (1.6)
A	EUF08368	e5gq9A2	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: EUF08368	ECOD (1.6)
A	Piwi_piwi-like_ProArk	e5gq9A6	A: a/b three-layered sandwiches	X: Middle domain in Argonaute homologs (From Topology)	H: Middle domain in Argonaute homologs (From Topology)	T: Middle domain in Argonaute homologs	F: Piwi_piwi-like_ProArk	ECOD (1.6)
A	Piwi_C_1	e5gq9A4	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Piwi_C_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth B]	3.30.530.60	Alpha Beta	2-Layer Sandwich	Alpha-D-Glucose-1,6-Bisphosphate	Chain A, domain 4	CATH (4.3.0)
D [auth B]	3.30.70.2620	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
D [auth B]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
D [auth B]	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
A	3.30.530.60	Alpha Beta	2-Layer Sandwich	Alpha-D-Glucose-1,6-Bisphosphate	Chain A, domain 4	CATH (4.3.0)
A	3.30.70.2620	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D], F	DNA (5'-D(PAPCPAPAPCPCPTPAPCPTPAPCPCPTPCPG)-3')	-	-	-
B [auth C], E	DNA (5'-D(PCPGPAPGPGPTPAPGPTPAPGPGPTPTPGPT)-3')	-	-	-
A, D [auth B]	Thermus thermophilus Argonaute	DNA binding binding nucleic acid binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity cation binding manganese ion binding transition metal ion binding ion binding DNA binding binding nucleic acid binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding hydrolase activity RNA binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response defense response to symbiont response to external stimulus nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response defense response to symbiont response to external stimulus clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids response to biotic stimulus defense response to other organism response to stress response to external biotic stimulus	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth B]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, D [auth B]	IPR040895	Argonaute, PAZ domain	Domain
A, D [auth B]	IPR054763	Argonaute, middle domain	Domain
A, D [auth B]	IPR003100	PAZ domain	Domain
A, D [auth B]	IPR054764	Argonaute, N-terminal domain, thermus	Domain
A, D [auth B]	IPR003165	Piwi domain	Domain
A, D [auth B]	IPR012337	Ribonuclease H-like superfamily	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.