4IUT | pdb_00004iut

crystal structure of SHH1 SAWADEE domain in complex with H3K9me2 peptide

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8092756	3000404	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8092757	3000404	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8092756	3000404	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8092757	3000404	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)
B	HSP70	e4iutB1	A: alpha bundles	X: all-alpha NTP pyrophosphatases	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: HSP70	ECOD (develop294)
B	tRNA-synt_2b	e4iutB2	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: tRNA-synt_2b	ECOD (develop294)
A	tRNA-synt_2b	e4iutA2	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: tRNA-synt_2b	ECOD (develop294)
A	N-glycanase_C	e4iutA4	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: N-glycanase_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
B	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
A	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
A	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF16719	SAWADEE domain (SAWADEE)	SAWADEE domain	The SAWADEE domain, found in plant homeobox proteins, has a pair of tandem tudor-like folds that bind chromatin [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Histone H3.2, H3(1-15)K9me3	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle extracellular region membraneless organelle intracellular membraneless organelle chromocenter cytosol cell periphery membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle extracellular region membraneless organelle intracellular membraneless organelle chromocenter cytosol cell periphery plasma membrane membrane protein-containing complex protein-DNA complex nucleosome chromatin chromosome nucleus
A, B	SAWADEE HOMEODOMAIN HOMOLOG 1	chromatin binding binding cation binding ion binding metal ion binding small molecule binding	regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process DNA methylation-dependent constitutive heterochromatin formation cellular process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process regulatory ncRNA-mediated gene silencing	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR009072	Histone-fold	Homologous Superfamily
C	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C	IPR000164	Histone H3/CENP-A	Family
A, B	IPR032001	SAWADEE domain	Domain
A, B	IPR039276	Protein SAWADEE HOMEODOMAIN HOMOLOG 1/2	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084

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.