6YCS | pdb_00006ycs

Human Transcription Cofactor PC4 DNA-binding domain in complex with full phosphorothioate 5-10-5 2'-O-methyl DNA gapmer antisense oligonucleotide.

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	ssDNA-binding transcriptional regulator domain	8034704	3000513	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ssDNA-binding transcriptional regulator domain	8034704	3000513	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ssDNA-binding transcriptional regulator domain	8034704	3000513	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ssDNA-binding transcriptional regulator domain	8034704	3000513	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)
D	PC4	e6ycsD1	A: a+b two layers	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain (From Topology)	T: ssDNA-binding transcriptional regulator domain	F: PC4	ECOD (1.6)
C	PC4	e6ycsC1	A: a+b two layers	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain (From Topology)	T: ssDNA-binding transcriptional regulator domain	F: PC4	ECOD (1.6)
B	PC4	e6ycsB1	A: a+b two layers	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain (From Topology)	T: ssDNA-binding transcriptional regulator domain	F: PC4	ECOD (1.6)
A	PC4	e6ycsA1	A: a+b two layers	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain (From Topology)	T: ssDNA-binding transcriptional regulator domain	F: PC4	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.30.31.10	Mainly Beta	Roll	Transcriptional Co-activator pc4	Chain A	CATH (utative)
C	2.30.31.10	Mainly Beta	Roll	Transcriptional Co-activator pc4	Chain A	CATH (utative)
B	2.30.31.10	Mainly Beta	Roll	Transcriptional Co-activator pc4	Chain A	CATH (utative)
A	2.30.31.10	Mainly Beta	Roll	Transcriptional Co-activator pc4	Chain A	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02229	Transcriptional Coactivator p15 (PC4) (PC4)	Transcriptional Coactivator p15 (PC4)	This domain is found at the C-terminal end of Activated RNA polymerase II transcriptional coactivator p15 from humans, YdbC from Lactococcus lactis, and other PC4 family members. p15 has a bipartite structure composed of an N-terminal regulatory doma ...	This domain is found at the C-terminal end of Activated RNA polymerase II transcriptional coactivator p15 from humans, YdbC from Lactococcus lactis, and other PC4 family members. p15 has a bipartite structure composed of an N-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain [1-4]. Activity is controlled by protein kinases that target the regulatory domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F	DNA (5'-D(P(OKQ))-D(P(OKT))-R(P(RFJ))-D((OKQ)P(OKT)P(AS)P(GS)P(OKN)P(OKN)P(PST)P(OKN)P(PST)P(GS)P(GS)P(AS)P(OKT)P*(OKT))-3')	-	-	-
E	DNA (5'-D(P(OKQ))-D(P(OKT))-R(P(RFJ))-D((OKQ)P(OKT)P(AS)P(GS)P(OKN)P(OKN)P(PST)P(OKN)P(PST)P(GS)P(GS)P(AS)P(OKT)P*(OKT))-3')	-	-	-
A, B, C, D	PC4 protein	DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription coactivator activity transcription regulator activity transcription coregulator activity DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding identical protein binding protein binding single-stranded DNA binding	regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription positive regulation of metabolic process regulation of DNA-templated transcription initiation regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription positive regulation of metabolic process regulation of DNA-templated transcription initiation regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process transcription initiation at RNA polymerase II promoter positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process positive regulation of transcription initiation by RNA polymerase II biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression positive regulation of transcription by RNA polymerase II macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation positive regulation of DNA-templated transcription initiation positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of transcription initiation by RNA polymerase II cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process promoter clearance during DNA-templated transcription RNA polymerase II promoter clearance negative regulation of metabolic process negative regulation of biological process DNA metabolic process negative regulation of cellular process negative regulation of DNA metabolic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of DNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex transcription regulator complex nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR009044	ssDNA-binding transcriptional regulator	Homologous Superfamily
A, B, C, D	IPR045125	RNA polymerase II transcriptional coactivator Sub1/Tcp4-like	Family
A, B, C, D	IPR003173	Transcriptional coactivator p15 (PC4), C-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P53999	tuberculosis astrocytic tumor breast carcinoma hypertensive disorder malignant pancreatic neoplasm ovarian cancer Pick disease psoriasis atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma nasopharyngeal carcinoma pancreatic ductal adenocarcinoma plasma cell myeloma Sjogren syndrome tuberculosis astrocytic tumor breast carcinoma hypertensive disorder malignant pancreatic neoplasm ovarian cancer Pick disease psoriasis atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma nasopharyngeal carcinoma pancreatic ductal adenocarcinoma plasma cell myeloma Sjogren syndrome breast cancer hereditary spastic paraplegia lung cancer osteosarcoma Parkinson disease pneumonia

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.