4DJA | pdb_00004dja

Crystal structure of a prokaryotic (6-4) photolyase PhrB from Agrobacterium Tumefaciens with an Fe-S cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore at 1.45A resolution

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	DPRP N-terminal domain-like	8045624	4004573	SCOP2 (2022-06-29)
A	SCOP2 Family	DPRP C-terminal domain-like	8051814	4007509	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleotidylyl transferase	8051813	3001541	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cryptochrome/photolyase FAD-binding domain	8051815	3000930	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DcpS_C	e4djaA2	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: DcpS_C	ECOD (develop294)
A	DPRP	e4djaA3	A: alpha bundles	X: P-loop domains-like	H: beta-helix of amnionless (AMN) extracellular domain	T: beta-helix of amnionless (AMN) extracellular domain	F: DPRP	ECOD (develop294)

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)
A	1.10.10.1710	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Deoxyribodipyrimidine photolyase-related	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF04244	Deoxyribodipyrimidine photo-lyase-related protein (DPRP)	Deoxyribodipyrimidine photo-lyase-related protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Photolyase	DNA binding binding nucleic acid binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding FAD binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding DNA binding binding nucleic acid binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding FAD binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding DNA (6-4) photolyase activity DNA photolyase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid lyase activity catalytic activity carbon-carbon lyase activity cation binding metal ion binding	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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036134	Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily	Homologous Superfamily
A	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A	IPR007357	Photolyase PhrB-like	Family
A	IPR052551	UV-induced DNA damage repair photolyase	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.