3VK0 | pdb_00003vk0

Crystal Structure of hypothetical transcription factor NHTF from Neisseria

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)
C	d3vk0c_	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
B	d3vk0b_	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
A	d3vk0a_	All alpha proteins	lambda repressor-like DNA-binding domains	lambda repressor-like DNA-binding domains	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8086833	3000119	SCOP2B (2022-06-29)
B	SCOP2 Family	SinR domain-like	8086832	4000896	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	lambda C1 repressor DNA-binding domain-like	8086833	3000119	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8086833	3000119	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)
C	Rrf2	e3vk0C1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: Rrf2	ECOD (develop294)
B	Rrf2	e3vk0B1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: Rrf2	ECOD (develop294)
A	Defensin_2	e3vk0A1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Defensin_2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
B	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)
A	1.10.260.40	Mainly Alpha	Orthogonal Bundle	434 Repressor (Amino-terminal Domain)	lambda repressor-like DNA-binding domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF01381	Helix-turn-helix (HTH_3)	Helix-turn-helix	This large family of DNA binding helix-turn helix proteins includes Cro Swiss:P03036 and CI Swiss:P03034. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be ...	This large family of DNA binding helix-turn helix proteins includes Cro Swiss:P03036 and CI Swiss:P03034. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteristic of the whole family [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Transcriptional regulator	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological 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 cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR050807	Transcriptional regulator/dioxygenase, bacterial-type	Family
A, B, C	IPR001387	Cro/C1-type, helix-turn-helix domain	Domain
A, B, C	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.