2VTB

Structure of cryptochrome 3 - DNA complex

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	FAD_binding_7	e2vtbA5	A: alpha complex topology	X: Cryptochrome/photolyase FAD-binding domain-related (From Homology)	H: Cryptochrome/photolyase FAD-binding domain-related	T: Cryptochrome/photolyase FAD-binding domain	F: FAD_binding_7	ECOD (1.6)
A	DNA_photolyase	e2vtbA6	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: DNA_photolyase	ECOD (1.6)
C	FAD_binding_7	e2vtbC3	A: alpha complex topology	X: Cryptochrome/photolyase FAD-binding domain-related (From Homology)	H: Cryptochrome/photolyase FAD-binding domain-related	T: Cryptochrome/photolyase FAD-binding domain	F: FAD_binding_7	ECOD (1.6)
C	DNA_photolyase	e2vtbC4	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: DNA_photolyase	ECOD (1.6)
D	FAD_binding_7	e2vtbD3	A: alpha complex topology	X: Cryptochrome/photolyase FAD-binding domain-related (From Homology)	H: Cryptochrome/photolyase FAD-binding domain-related	T: Cryptochrome/photolyase FAD-binding domain	F: FAD_binding_7	ECOD (1.6)
D	DNA_photolyase	e2vtbD4	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: DNA_photolyase	ECOD (1.6)
E	FAD_binding_7	e2vtbE3	A: alpha complex topology	X: Cryptochrome/photolyase FAD-binding domain-related (From Homology)	H: Cryptochrome/photolyase FAD-binding domain-related	T: Cryptochrome/photolyase FAD-binding domain	F: FAD_binding_7	ECOD (1.6)
E	DNA_photolyase	e2vtbE4	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: DNA_photolyase	ECOD (1.6)
F	FAD_binding_7	e2vtbF3	A: alpha complex topology	X: Cryptochrome/photolyase FAD-binding domain-related (From Homology)	H: Cryptochrome/photolyase FAD-binding domain-related	T: Cryptochrome/photolyase FAD-binding domain	F: FAD_binding_7	ECOD (1.6)
F	DNA_photolyase	e2vtbF4	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: DNA_photolyase	ECOD (1.6)
B	FAD_binding_7	e2vtbB3	A: alpha complex topology	X: Cryptochrome/photolyase FAD-binding domain-related (From Homology)	H: Cryptochrome/photolyase FAD-binding domain-related	T: Cryptochrome/photolyase FAD-binding domain	F: FAD_binding_7	ECOD (1.6)
B	DNA_photolyase	e2vtbB4	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: DNA_photolyase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
A	1.25.40.80	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A	1.10.579.10	Mainly Alpha	Orthogonal Bundle	DNA Cyclobutane Dipyrimidine Photolyase, subunit A	domain 3	CATH (4.3.0)
C	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
C	1.25.40.80	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
C	1.10.579.10	Mainly Alpha	Orthogonal Bundle	DNA Cyclobutane Dipyrimidine Photolyase, subunit A	domain 3	CATH (4.3.0)
D	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
D	1.25.40.80	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
D	1.10.579.10	Mainly Alpha	Orthogonal Bundle	DNA Cyclobutane Dipyrimidine Photolyase, subunit A	domain 3	CATH (4.3.0)
E	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
E	1.25.40.80	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
E	1.10.579.10	Mainly Alpha	Orthogonal Bundle	DNA Cyclobutane Dipyrimidine Photolyase, subunit A	domain 3	CATH (4.3.0)
F	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
F	1.25.40.80	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
F	1.10.579.10	Mainly Alpha	Orthogonal Bundle	DNA Cyclobutane Dipyrimidine Photolyase, subunit A	domain 3	CATH (4.3.0)
B	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B	1.25.40.80	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
B	1.10.579.10	Mainly Alpha	Orthogonal Bundle	DNA Cyclobutane Dipyrimidine Photolyase, subunit A	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, D, E, F	PF00875	DNA photolyase (DNA_photolyase)	DNA photolyase	This domain binds a light harvesting cofactor.	Domain
A, C, D, E, F	PF03441	FAD binding domain of DNA photolyase (FAD_binding_7)	FAD binding domain of DNA photolyase	-	Domain
B	PF00875	DNA photolyase (DNA_photolyase)	DNA photolyase	This domain binds a light harvesting cofactor.	Domain
B	PF03441	FAD binding domain of DNA photolyase (FAD_binding_7)	FAD binding domain of DNA photolyase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, D, E, F	CRYPTOCHROME DASH	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding DNA photolyase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid deoxyribodipyrimidine photo-lyase activity lyase activity catalytic activity carbon-carbon lyase activity FAD binding flavin adenine dinucleotide binding molecular transducer activity photoreceptor activity signaling receptor activity	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process pyrimidine dimer repair macromolecule metabolic process photoreactive repair cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process pyrimidine dimer repair macromolecule metabolic process photoreactive repair DNA repair	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle plastid chloroplast
B	CRYPTOCHROME DASH	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding DNA photolyase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid deoxyribodipyrimidine photo-lyase activity lyase activity catalytic activity carbon-carbon lyase activity FAD binding flavin adenine dinucleotide binding molecular transducer activity photoreceptor activity signaling receptor activity	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process pyrimidine dimer repair macromolecule metabolic process photoreactive repair cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process pyrimidine dimer repair macromolecule metabolic process photoreactive repair DNA repair	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle plastid chloroplast
G, H, I, J, K G, H, I, J, K, L	5'-D(DTDTDTDT*DTP)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, D, E, F	IPR014133	Cryptochrome DASH	Family
A, C, D, E, F	IPR002081	Cryptochrome/DNA photolyase class 1	Family
A, C, D, E, F	IPR036134	Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily	Homologous Superfamily
A, C, D, E, F	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A, C, D, E, F	IPR036155	Cryptochrome/photolyase, N-terminal domain superfamily	Homologous Superfamily
A, C, D, E, F	IPR006050	DNA photolyase, N-terminal	Domain
A, C, D, E, F	IPR005101	Cryptochrome/DNA photolyase, FAD-binding domain	Domain
B	IPR014133	Cryptochrome DASH	Family
B	IPR002081	Cryptochrome/DNA photolyase class 1	Family
B	IPR036134	Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily	Homologous Superfamily
B	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
B	IPR036155	Cryptochrome/photolyase, N-terminal domain superfamily	Homologous Superfamily
B	IPR006050	DNA photolyase, N-terminal	Domain
B	IPR005101	Cryptochrome/DNA photolyase, FAD-binding 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.