3A4K | pdb_00003a4k

Crystal structural analysis of HindIII restriction endonuclease in complex with cognate DNA and divalent cations at 2.17 angstrom 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)
D	SCOP2B Superfamily	Restriction endonuclease-like	8054056	3000104	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Restriction endonuclease-like	8054056	3000104	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Restriction endonuclease-like	8054056	3000104	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Restriction endonuclease-like	8054056	3000104	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	PDEase_I	e3a4kD1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (v294.1)
C [auth B]	PDEase_I	e3a4kB1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (v294.1)
B [auth C]	PDEase_I	e3a4kC1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PDEase_I	ECOD (v294.1)
A	RE_HindIII	e3a4kA1	A: a/b three-layered sandwiches	X: Metallothionein	H: Metallothionein	T: Metallothionein	F: RE_HindIII	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.91.70	Alpha Beta	3-Layer(aba) Sandwich	Restriction Endonuclease	Type II restriction endonuclease, HindIII	CATH (4.3.0)
D	6.10.250.1510	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
C [auth B]	3.40.91.70	Alpha Beta	3-Layer(aba) Sandwich	Restriction Endonuclease	Type II restriction endonuclease, HindIII	CATH (4.3.0)
C [auth B]	6.10.250.1510	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B [auth C]	3.40.91.70	Alpha Beta	3-Layer(aba) Sandwich	Restriction Endonuclease	Type II restriction endonuclease, HindIII	CATH (4.3.0)
B [auth C]	6.10.250.1510	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	3.40.91.70	Alpha Beta	3-Layer(aba) Sandwich	Restriction Endonuclease	Type II restriction endonuclease, HindIII	CATH (4.3.0)
A	6.10.250.1510	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth B], D	PF09518	HindIII restriction endonuclease (RE_HindIII)	HindIII restriction endonuclease	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
M, N	DNA (5'-D(GPCPCPAPAPGPCPTPTPGPGPC)-3')	-	-	-
F, H, J, L	DNA (5'-D(PAPGPCPTPTPGPGPC)-3')	-	-	-
E, G, I, K	DNA (5'-D(GPCPCPA)-3')	-	-	-
A, B [auth C], C [auth B], D	Type-2 restriction enzyme HindIII	endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity type II site-specific deoxyribonuclease activity restriction endodeoxyribonuclease activity DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response DNA restriction-modification system defense response to symbiont response to external stimulus primary metabolic process clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids DNA metabolic process response to biotic stimulus nucleic acid metabolic process nucleobase-containing compound metabolic process DNA modification biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response DNA restriction-modification system defense response to symbiont response to external stimulus primary metabolic process clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids DNA metabolic process response to biotic stimulus nucleic acid metabolic process nucleobase-containing compound metabolic process DNA modification defense response to other organism response to stress macromolecule modification metabolic process cellular process response to external biotic stimulus macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth B], D	IPR019043	Restriction endonuclease, type II, HindIII	Family
A, B [auth C], C [auth B], D	IPR038373	Restriction endonuclease, type II, HindIII 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.