4ES4 | pdb_00004es4

Crystal structure of YdiV and FlhD complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d4es4h_	All alpha proteins	Flagellar transcriptional activator FlhD	Flagellar transcriptional activator FlhD	Flagellar transcriptional activator FlhD	Flagellar transcriptional activator FlhD	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
F	d4es4f_	All alpha proteins	Flagellar transcriptional activator FlhD	Flagellar transcriptional activator FlhD	Flagellar transcriptional activator FlhD	Flagellar transcriptional activator FlhD	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d4es4d_	All alpha proteins	Flagellar transcriptional activator FlhD	Flagellar transcriptional activator FlhD	Flagellar transcriptional activator FlhD	Flagellar transcriptional activator FlhD	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4es4b_	All alpha proteins	Flagellar transcriptional activator FlhD	Flagellar transcriptional activator FlhD	Flagellar transcriptional activator FlhD	Flagellar transcriptional activator FlhD	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Flagellar transcriptional activator FlhD	8032668	3000232	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Flagellar transcriptional activator FlhD	8032668	3000232	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Flagellar transcriptional activator FlhD	8032668	3000232	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Flagellar transcriptional activator FlhD	8032668	3000232	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)
H	SmpA_OmlA	e4es4H1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)
F	SmpA_OmlA	e4es4F1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)
D	SmpA_OmlA	e4es4D1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)
B	Aldo_ket_red	e4es4B1	A: a/b three-layered sandwiches	X: Globin-like	H: Nucleoside diphosphate kinases	T: Nucleoside diphosphate kinases	F: Aldo_ket_red	ECOD (v294.1)
G	Fpg-like_C	e4es4G2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Fpg-like_C	ECOD (v294.1)
E	VHP	e4es4E1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Notch heterodimerization domain	T: Notch heterodimerization domain	F: VHP	ECOD (v294.1)
C	Fpg-like_C	e4es4C2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Fpg-like_C	ECOD (v294.1)
A	LYTB	e4es4A1	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: LYTB	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	1.10.4000.10	Mainly Alpha	Orthogonal Bundle	Flagellar transcriptional activator fold	Flagellar transcriptional activator FlhD	CATH (4.3.0)
F	1.10.4000.10	Mainly Alpha	Orthogonal Bundle	Flagellar transcriptional activator fold	Flagellar transcriptional activator FlhD	CATH (4.3.0)
D	1.10.4000.10	Mainly Alpha	Orthogonal Bundle	Flagellar transcriptional activator fold	Flagellar transcriptional activator FlhD	CATH (4.3.0)
B	1.10.4000.10	Mainly Alpha	Orthogonal Bundle	Flagellar transcriptional activator fold	Flagellar transcriptional activator FlhD	CATH (4.3.0)
G	3.20.20.450	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	EAL domain	CATH (4.3.0)
E	3.20.20.450	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	EAL domain	CATH (4.3.0)
C	3.20.20.450	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	EAL domain	CATH (4.3.0)
A	3.20.20.450	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	EAL domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF05247	Flagellar transcriptional activator (FlhD) (FlhD)	Flagellar transcriptional activator (FlhD)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	Flagellar transcriptional regulator FlhD	DNA binding binding nucleic acid binding	organelle assembly cell projection organization bacterial-type flagellum assembly membraneless organelle assembly cellular component biogenesis cellular component organization bacterial-type flagellum organization organelle organization cellular component assembly cellular process cellular component organization or biogenesis cell projection assembly positive regulation of organelle organization regulation of cellular process organelle assembly cell projection organization bacterial-type flagellum assembly membraneless organelle assembly cellular component biogenesis cellular component organization bacterial-type flagellum organization organelle organization cellular component assembly cellular process cellular component organization or biogenesis cell projection assembly positive regulation of organelle organization regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization positive regulation of biological process positive regulation of cell projection organization positive regulation of cellular process regulation of bacterial-type flagellum assembly regulation of biological process positive regulation of cellular component biogenesis regulation of cell projection assembly regulation of cell projection organization positive regulation of bacterial-type flagellum assembly biological regulation regulation of cellular component biogenesis regulation of organelle organization regulation of organelle assembly positive regulation of organelle assembly RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	protein-containing complex transcription regulator complex cellular anatomical structure intracellular anatomical structure cytoplasm
A, C, E, G	Putative cyclic di-GMP regulator CdgR	phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity cyclic-guanylate-specific phosphodiesterase activity hydrolase activity catalytic activity	regulation of bacterial-type flagellum-dependent cell motility negative regulation of locomotion regulation of biological process regulation of cell motility regulation of cellular process biological regulation negative regulation of biological process archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility regulation of locomotion negative regulation of cellular process negative regulation of cell motility cellular process bacterial-type flagellum-dependent cell motility regulation of bacterial-type flagellum-dependent cell motility negative regulation of locomotion regulation of biological process regulation of cell motility regulation of cellular process biological regulation negative regulation of biological process archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility regulation of locomotion negative regulation of cellular process negative regulation of cell motility cellular process bacterial-type flagellum-dependent cell motility cell motility negative regulation of bacterial-type flagellum-dependent cell motility locomotion cell aggregation biofilm formation regulation of single-species biofilm formation biological process involved in intraspecies interaction between organisms single-species biofilm formation aggregation of unicellular organisms	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR023559	Flagellar transcriptional activator FlhD	Family
B, D, F, H	IPR036194	Flagellar transcriptional activator FlhD superfamily	Homologous Superfamily
A, C, E, G	IPR050706	Cyclic-di-GMP_PDE-like	Unknown
A, C, E, G	IPR001633	EAL domain	Domain
A, C, E, G	IPR035919	EAL 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.