6FAS | pdb_00006fas

Crystal structure of VAL1 B3 domain in complex with cognate DNA

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	B3 DNA binding domain	8089661	4003270	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA-binding pseudobarrel domain	8089662	3000213	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	DNA-binding pseudobarrel domain	8089662	3000213	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)
A	V-set	e6fasA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
B	Ras	e6fasB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Rubredoxin-related	F: Ras	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.330.10	Mainly Beta	Beta Barrel	At1g16640 B3 domain	DNA-binding pseudobarrel domain	CATH (4.3.0)
B	2.40.330.10	Mainly Beta	Beta Barrel	At1g16640 B3 domain	DNA-binding pseudobarrel domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02362	B3 DNA binding domain (B3)	B3 DNA binding domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, F	DNA (5'-D(CPGPGPTPGPCPAPTPGPGPCPT)-3')	-	-	-
C, E	DNA (5'-D(APGPCPCPAPTPGPCPAPCPCPG)-3')	-	-	-
A, B	B3 domain-containing transcription repressor VAL1	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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 response to abscisic acid response to stimulus response to lipid response to hormone response to alcohol response to chemical response to endogenous stimulus response to oxygen-containing compound response to carbohydrate response to sucrose response to disaccharide	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR015300	DNA-binding pseudobarrel domain superfamily	Homologous Superfamily
A, B	IPR003340	B3 DNA binding domain	Domain
A, B	IPR057743	VAL1-3, N-terminal zinc finger domain	Domain
A, B	IPR011124	Zinc finger, CW-type	Domain

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.