3GOD | pdb_00003god

Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated antiviral defense

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	d3godd_	Multi-domain proteins (alpha and beta)	CRISPR associated protein Cas1-like	CRISPR associated protein Cas1-like	CRISPR associated protein Cas1-like	Cas1	(Pseudomonas aeruginosa UCBPP-PA14 ) [TaxId: 208963 ],	SCOPe (2.08)
C	d3godc_	Multi-domain proteins (alpha and beta)	CRISPR associated protein Cas1-like	CRISPR associated protein Cas1-like	CRISPR associated protein Cas1-like	Cas1	(Pseudomonas aeruginosa UCBPP-PA14 ) [TaxId: 208963 ],	SCOPe (2.08)
B	d3godb_	Multi-domain proteins (alpha and beta)	CRISPR associated protein Cas1-like	CRISPR associated protein Cas1-like	CRISPR associated protein Cas1-like	Cas1	(Pseudomonas aeruginosa UCBPP-PA14 ) [TaxId: 208963 ],	SCOPe (2.08)
A	d3goda_	Multi-domain proteins (alpha and beta)	CRISPR associated protein Cas1-like	CRISPR associated protein Cas1-like	CRISPR associated protein Cas1-like	Cas1	(Pseudomonas aeruginosa UCBPP-PA14 ) [TaxId: 208963 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	CRISPR associated protein Cas1	8053181	3002164	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CRISPR associated protein Cas1	8053181	3002164	SCOP2B (2022-06-29)
B	SCOP2 Family	CRISPR associated protein Cas1	8049657	4006578	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	CRISPR associated protein Cas1	8053181	3002164	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	CRISPR associated protein Cas1	8053181	3002164	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	Ribosomal_L36	e3godD1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: Ribosomal_L36	ECOD (v294.1)
C	CoV_NSP4_C	e3godC2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: CoV_NSP4_C	ECOD (v294.1)
B	Ribosomal_L36	e3godB1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: Ribosomal_L36	ECOD (v294.1)
A	Peptidase_S74	e3godA1	A: a/b three-layered sandwiches	X: Intramolecular chaperone domain in virus tail spike protein	H: Intramolecular chaperone domain in virus tail spike protein	T: Intramolecular chaperone domain in virus tail spike protein	F: Peptidase_S74	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.100.10.20	Alpha Beta	Ribosomal Protein L15	Chain: K	domain 2	CATH (4.3.0)
D	1.20.120.920	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	CRISPR-associated endonuclease Cas1, C-terminal domain	CATH (4.3.0)
C	3.100.10.20	Alpha Beta	Ribosomal Protein L15	Chain: K	domain 2	CATH (4.3.0)
C	1.20.120.920	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	CRISPR-associated endonuclease Cas1, C-terminal domain	CATH (4.3.0)
B	3.100.10.20	Alpha Beta	Ribosomal Protein L15	Chain: K	domain 2	CATH (4.3.0)
B	1.20.120.920	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	CRISPR-associated endonuclease Cas1, C-terminal domain	CATH (4.3.0)
A	3.100.10.20	Alpha Beta	Ribosomal Protein L15	Chain: K	domain 2	CATH (4.3.0)
A	1.20.120.920	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	CRISPR-associated endonuclease Cas1, C-terminal domain	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Cas1	DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity DNA binding binding nucleic acid binding hydrolase activity cation binding ion binding metal ion 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 DNA binding binding nucleic acid binding hydrolase activity cation binding ion binding metal ion binding small molecule binding identical protein binding protein binding	biological process involved in interspecies interaction between organisms defense response to virus response to stimulus defense response response to other organism response to stress response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus maintenance of CRISPR repeat elements chromosome organization primary metabolic process DNA metabolic process biological process involved in interspecies interaction between organisms defense response to virus response to stimulus defense response response to other organism response to stress response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus maintenance of CRISPR repeat elements chromosome organization primary metabolic process DNA metabolic process maintenance of DNA repeat elements nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process organelle organization cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002729	CRISPR-associated protein Cas1	Family
A, B, C, D	IPR042206	CRISPR-associated endonuclease Cas1, C-terminal domain	Homologous Superfamily
A, B, C, D	IPR042211	CRISPR-associated endonuclease Cas1, N-terminal domain	Homologous Superfamily
A, B, C, D	IPR050646	CRISPR-associated endonuclease Cas1	Family
A, B, C, D	IPR019857	CRISPR-associated protein Cas1, YPEST subtype	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.