5TZF | pdb_00005tzf

Structure of the BldD CTD(D116A)-(c-di-GMP)2 intermediate, form 1

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)
E [auth I]	Glyco_hydro_77	e5tzfI1	A: a/b three-layered sandwiches	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.1)
F [auth H]	Glyco_hydro_77	e5tzfH1	A: a/b three-layered sandwiches	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.1)
H [auth M]	Glyco_hydro_77	e5tzfM1	A: a/b three-layered sandwiches	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.1)
G [auth N]	Glyco_hydro_77	e5tzfN1	A: a/b three-layered sandwiches	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.1)
D	Glyco_hydro_77	e5tzfD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.1)
C [auth E]	Glyco_hydro_77	e5tzfE1	A: a/b three-layered sandwiches	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.1)
B	Glyco_hydro_77	e5tzfB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.1)
A [auth J]	Glyco_hydro_77	e5tzfJ1	A: a/b three-layered sandwiches	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Glyco_hydro_77	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth I]	1.10.10.1930	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
F [auth H]	1.10.10.1930	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
H [auth M]	1.10.10.1930	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
G [auth N]	1.10.10.1930	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
D	1.10.10.1930	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
C [auth E]	1.10.10.1930	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
B	1.10.10.1930	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
A [auth J]	1.10.10.1930	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth J], B, C [auth E], D, E [auth I], A [auth J], B, C [auth E], D, E [auth I], F [auth H], G [auth N], H [auth M]	PF21179	DNA-binding protein BldD-like, C-terminal domain (BldD-like_C)	DNA-binding protein BldD-like, C-terminal domain	This domain is found at the C-terminal end of DNA-binding protein BldD from Streptomyces venezuelae (Swiss:F2RCL8) and similar proteins found in Actinobacteria. This domain shows two beta-alpha- alpha repeats and a short C-terminal helix. It is respo ...	This domain is found at the C-terminal end of DNA-binding protein BldD from Streptomyces venezuelae (Swiss:F2RCL8) and similar proteins found in Actinobacteria. This domain shows two beta-alpha- alpha repeats and a short C-terminal helix. It is responsible for the binding of the protein to the second messenger 3',5'-cyclic diguanylic acid (c-di-GMP) [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth J], B, C [auth E], D, E [auth I], A [auth J], B, C [auth E], D, E [auth I], F [auth H], G [auth N], H [auth M]	DNA-binding protein	DNA binding binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth J], B, C [auth E], D, E [auth I], A [auth J], B, C [auth E], D, E [auth I], F [auth H], G [auth N], H [auth M]	IPR038099	BldD-like, C-terminal domain superfamily	Homologous Superfamily
A [auth J], B, C [auth E], D, E [auth I], A [auth J], B, C [auth E], D, E [auth I], F [auth H], G [auth N], H [auth M]	IPR037664	BldD, C-terminal	Domain
A [auth J], B, C [auth E], D, E [auth I], A [auth J], B, C [auth E], D, E [auth I], F [auth H], G [auth N], H [auth M]	IPR001387	Cro/C1-type, helix-turn-helix domain	Domain
A [auth J], B, C [auth E], D, E [auth I], A [auth J], B, C [auth E], D, E [auth I], F [auth H], G [auth N], H [auth M]	IPR010982	Lambda repressor-like, DNA-binding domain 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.