6CW3 | pdb_00006cw3

Crystal structure of a yeast SAGA transcriptional coactivator Ada2/Gcn5 HAT subcomplex, crystal form 2

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
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)
D	d6cw3d2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6cw3d1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6cw3b2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6cw3b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6cw3c_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6cw3a_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G [auth H]	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8036007	3000403	SCOP2B (2022-06-29)
E [auth F]	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8036007	3000403	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 [auth G]	Anoctamin	e6cw3G1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Anoctamin	ECOD (develop294)
F [auth E]	Flu_PB2_1st	e6cw3E1	A: alpha bundles	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: Flu_PB2_1st	ECOD (develop294)
E [auth F]	HATPase_c_5	e6cw3F01	A: alpha bundles	X: Rossmann-like	H: P-loop domains-related	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: HATPase_c_5	ECOD (develop294)
D	Anoctamin	e6cw3D1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Anoctamin	ECOD (develop294)
B	Anoctamin	e6cw3B1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Anoctamin	ECOD (develop294)
C	Flu_PB2_1st	e6cw3C1	A: alpha bundles	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: Flu_PB2_1st	ECOD (develop294)
A	Anoctamin	e6cw3A1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Anoctamin	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B, D	Antibody Fab Fragment	L-KAPPA	Homo sapiens (human)	IGKV1D-1301, IGKV1-1302, IGKV1D-1302, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)
A, C	Antibody Fab Fragment	VH-CH1	Homo sapiens (human)	IGHV3-6601, IGHV3-6602, IGHV3-6604, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D	Light Chain	IGKV1	Kappa	histone acetyltransferase gcn5 \| transcriptional adapter 2	SAbDab (2026-03-20)
A, C	Heavy Chain	IGHV3	-	histone acetyltransferase gcn5 \| transcriptional adapter 2	SAbDab (2026-03-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
F [auth E], H [auth G]	PF00249	Myb-like DNA-binding domain (Myb_DNA-binding)	Myb-like DNA-binding domain	This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family [1].	Domain
F [auth E], H [auth G]	PF00569	Zinc finger, ZZ type (ZZ)	Zinc finger, ZZ type	Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin. Putative zinc finger; binding not yet shown. Four to six cysteine residues in its sequence are responsible for coordinating zinc ions, to reinforce the structure [2].	Domain
E [auth F], G [auth H]	PF00583	Acetyltransferase (GNAT) family (Acetyltransf_1)	Acetyltransferase (GNAT) family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth E], H [auth G]	Transcriptional adapter 2	chromatin binding binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding modified amino acid binding chromatin binding binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding modified amino acid binding anion binding phospholipid binding lipid binding phosphatidylserine binding	cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process replication-born double-strand break repair via sister chromatid exchange cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process replication-born double-strand break repair via sister chromatid exchange cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair subtelomeric heterochromatin formation 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 negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process regulation of metabolic process RNA metabolic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process regulation of DNA-templated transcription nucleolar chromatin organization rDNA heterochromatin formation nucleus organization organelle organization nucleolus organization facultative heterochromatin formation	protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex SAGA-type complex SLIK (SAGA-like) complex intracellular protein-containing complex peptidase complex SAGA complex ADA complex chromosome, telomeric region chromosomal region membrane-bounded organelle nucleus intracellular membrane-bounded organelle
E [auth F], G [auth H]	Histone acetyltransferase GCN5	histone H4K12ac reader activity histone reader activity histone H4 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity transcription regulator activity transcription coregulator activity protein-lysine-acetyltransferase activity catalytic activity, acting on a protein protein N-acetyltransferase activity acyltransferase activity N-acetyltransferase activity transferase activity histone H4K12ac reader activity histone reader activity histone H4 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity transcription regulator activity transcription coregulator activity protein-lysine-acetyltransferase activity catalytic activity, acting on a protein protein N-acetyltransferase activity acyltransferase activity N-acetyltransferase activity transferase activity protein N-acyltransferase activity histone acetyltransferase activity acetyltransferase activity histone modifying activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity N-acyltransferase activity histone H4K16ac reader activity peptide crotonyltransferase activity histone crotonyltransferase activity histone H3K56ac reader activity histone H3 reader activity histone H3 acetyltransferase 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 transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of biological 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 transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II 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 transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process DNA-templated transcription elongation positive regulation of RNA biosynthetic process cellular component organization chromatin organization cellular component organization or biogenesis chromatin remodeling	protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex intracellular protein-containing complex cytoplasm cytosol chromosome, centromeric region chromosomal region SAGA-type complex SLIK (SAGA-like) complex peptidase complex SAGA complex ADA complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B, D	antibody light chain	-	-	-
A, C	antibody heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth E], H [auth G]	IPR043145	Zinc finger, ZZ-type superfamily	Homologous Superfamily
F [auth E], H [auth G]	IPR000433	Zinc finger, ZZ-type	Domain
F [auth E], H [auth G]	IPR041983	ADA2-like, zinc finger, ZZ-type	Domain
F [auth E], H [auth G]	IPR016827	Transcriptional adaptor 2	Family
F [auth E], H [auth G]	IPR009057	Homedomain-like superfamily	Homologous Superfamily
F [auth E], H [auth G]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
F [auth E], H [auth G]	IPR017884	SANT domain	Domain
F [auth E], H [auth G]	IPR001005	SANT/Myb domain	Domain
F [auth E], H [auth G]	IPR007526	SWIRM domain	Domain
F [auth E], H [auth G]	IPR055141	Transcriptional adapter 2-alpha/beta-like domain	Domain
E [auth F], G [auth H]	IPR018359	Bromodomain, conserved site	Conserved Site
E [auth F], G [auth H]	IPR000182	GNAT domain	Domain
E [auth F], G [auth H]	IPR001487	Bromodomain	Domain
E [auth F], G [auth H]	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
E [auth F], G [auth H]	IPR016181	Acyl-CoA N-acyltransferase	Homologous Superfamily
E [auth F], G [auth H]	IPR037800	Histone acetyltransferase GCN5	Family

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.