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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6YCS

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

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003677	molecular_function	DNA binding
A	0003713	molecular_function	transcription coactivator activity
A	0006355	biological_process	regulation of DNA-templated transcription
A	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II
B	0003677	molecular_function	DNA binding
B	0003713	molecular_function	transcription coactivator activity
B	0006355	biological_process	regulation of DNA-templated transcription
B	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II
C	0003677	molecular_function	DNA binding
C	0003713	molecular_function	transcription coactivator activity
C	0006355	biological_process	regulation of DNA-templated transcription
C	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II
D	0003677	molecular_function	DNA binding
D	0003713	molecular_function	transcription coactivator activity
D	0006355	biological_process	regulation of DNA-templated transcription
D	0060261	biological_process	positive regulation of transcription initiation by RNA polymerase II

Functional Information from PDB Data

site_id	AC1
Number of Residues	2
Details	binding site for residue SO4 A 201

Chain	Residue
A	ARG100
E	HOH201

site_id	AC2
Number of Residues	3
Details	binding site for residue NA E 101

Chain	Residue
A	ARG100
E	GS13
E	GS14

site_id	AC3
Number of Residues	11
Details	binding site for residues OKT E 2 and RFJ E 3

Chain	Residue
B	ARG100
C	ARG100
D	ARG100
E	OKQ4
F	OKN8
F	PST10
F	PST12
B	ARG86
B	TRP89
B	PRO98
B	GLY99

site_id	AC4
Number of Residues	14
Details	binding site for residues RFJ E 3 and OKQ E 4

Chain	Residue
A	ARG100
A	LYS101
B	LEU82
B	ARG86
B	PRO98
B	GLY99
B	ARG100
C	ARG100
D	ARG100
E	OKT2
E	OKT5
F	GS7
F	OKN8
F	PST10

site_id	AC5
Number of Residues	11
Details	binding site for residues OKQ E 4 and OKT E 5

Chain	Residue
A	ARG70
A	ARG100
A	LYS101
B	PHE77
B	LEU82
B	ARG86
E	RFJ3
E	PPS6
F	PPS6
F	GS7
F	OKN8

site_id	AC6
Number of Residues	12
Details	binding site for residues GS E 7 and OKN E 8

Chain	Residue
A	ILE66
A	GLY67
A	LYS68
B	ASN106
B	GLU108
B	GLN109
E	PPS6
E	OKN9
E	HOH201
F	RFJ3
F	OKQ4
F	OKT5

site_id	AC7
Number of Residues	15
Details	binding site for residues OKN E 8 and OKN E 9

Chain	Residue
A	GLN65
A	ILE66
A	GLY67
A	LYS68
B	ASN106
B	GLU108
B	GLN109
B	GLN112
C	PHE77
E	GS7
E	PST10
E	OKN11
E	HOH202
F	OKT2
F	RFJ3

site_id	AC8
Number of Residues	12
Details	binding site for residues OKN E 9 and PST E 10

Chain	Residue
A	GLN65
A	ILE66
A	GLY67
B	GLN112
C	ARG75
C	PHE77
C	LYS78
E	OKN8
E	OKN11
E	HOH202
F	OKT2
F	RFJ3

site_id	AC9
Number of Residues	6
Details	binding site for residues PST E 10 and OKN E 11

Chain	Residue
C	ARG75
C	PHE77
C	LYS78
E	OKN9
E	PST12
F	OKT2

site_id	AD1
Number of Residues	8
Details	binding site for residues OKN E 11 and PST E 12

Chain	Residue
A	TRP89
A	MET90
A	PRO92
C	LYS97
E	OKN9
E	PST10
E	GS13
F	OKT2

site_id	AD2
Number of Residues	14
Details	binding site for residues PST E 12 and GS E 13

Chain	Residue
C	ASP91
C	PRO92
C	GLU95
C	LYS97
E	OKN11
E	GS14
E	NA101
F	OKQ1
F	OKT2
A	TRP89
A	MET90
A	PRO92
A	PRO98
A	ARG100

site_id	AD3
Number of Residues	15
Details	binding site for residues GS E 13 and GS E 14

Chain	Residue
A	SER73
A	ARG75
A	ARG86
A	TYR88
A	TRP89
A	PRO98
A	GLY99
A	ARG100
C	ASP91
C	PRO92
C	GLU95
E	PST12
E	PPS15
E	NA101
F	OKQ1

site_id	AD4
Number of Residues	6
Details	binding site for residues OKT E 16 and OKT E 17

Chain	Residue
A	LYS80
A	LEU82
A	ASN106
B	ARG70
B	LYS101
E	PPS15

site_id	AD5
Number of Residues	11
Details	binding site for residues OKQ F 1 and OKT F 2

Chain	Residue
A	ARG100
C	ARG86
C	TRP89
C	PRO98
C	GLY99
C	ARG100
E	OKN9
E	OKN11
E	PST12
E	GS13
F	RFJ3

site_id	AD6
Number of Residues	11
Details	binding site for residues OKQ F 1 and OKT F 2

Chain	Residue
A	ARG100
C	ARG86
C	TRP89
C	PRO98
C	GLY99
C	ARG100
E	OKN9
E	OKN11
E	PST12
E	GS13
F	RFJ3

site_id	AD7
Number of Residues	15
Details	binding site for residues OKT F 2 and RFJ F 3

Chain	Residue
C	ARG75
C	PHE77
C	LEU82
C	ARG86
C	GLY99
C	ARG100
C	SER104
C	HOH201
E	GS7
E	OKN8
E	OKN9
E	OKN11
E	PST12
F	OKQ1
F	OKQ4

site_id	AD8
Number of Residues	13
Details	binding site for residues RFJ F 3 and OKQ F 4

Chain	Residue
C	ARG75
C	PHE77
C	LEU82
C	ARG86
C	SER104
C	HOH201
D	ARG70
D	LYS101
E	GS7
E	OKN8
E	OKN9
F	OKT2
F	OKT5

site_id	AD9
Number of Residues	8
Details	binding site for residues OKQ F 4 and OKT F 5

Chain	Residue
C	PHE77
C	SER104
D	ARG70
D	LYS101
E	PPS6
E	GS7
F	RFJ3
F	PPS6

site_id	AE1
Number of Residues	5
Details	binding site for residues GS F 7 and OKN F 8

Chain	Residue
E	RFJ3
E	OKQ4
E	OKT5
F	PPS6
F	PST10

site_id	AE2
Number of Residues	12
Details	binding site for residues PST F 10 and OKN F 11

Chain	Residue
B	GLU93
B	LYS97
D	ARG75
D	ASP84
D	ARG86
D	TRP89
D	PRO98
D	GLY99
D	ARG100
E	RFJ3
F	OKN8
F	PST12

site_id	AE3
Number of Residues	14
Details	binding site for residues OKN F 11 and PST F 12

Chain	Residue
B	GLU93
B	LYS97
C	ARG100
D	ARG75
D	PHE77
D	ASP84
D	ARG86
D	PRO98
D	GLY99
D	ARG100
D	SER104
E	OKT2
F	PST10
F	GS13

site_id	AE4
Number of Residues	10
Details	binding site for residues PST F 12 and GS F 13

Chain	Residue
B	GLU93
C	ARG70
C	ARG100
C	LYS101
D	ARG75
D	PHE77
D	ARG86
D	SER104
E	OKT2
F	OKN11

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	72
Details	Region: {"description":"Interaction with ssDNA"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Modified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"21406692","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	8
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

244693

PDB entries from 2025-11-12

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