6YOV

OCT4-SOX2-bound nucleosome - SHL+6

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000786	cellular_component	nucleosome
A	0003677	molecular_function	DNA binding
A	0005515	molecular_function	protein binding
A	0005576	cellular_component	extracellular region
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005694	cellular_component	chromosome
A	0006325	biological_process	chromatin organization
A	0006334	biological_process	nucleosome assembly
A	0010467	biological_process	gene expression
A	0016020	cellular_component	membrane
A	0030527	molecular_function	structural constituent of chromatin
A	0032200	biological_process	telomere organization
A	0032991	cellular_component	protein-containing complex
A	0040029	biological_process	epigenetic regulation of gene expression
A	0043229	cellular_component	intracellular organelle
A	0045296	molecular_function	cadherin binding
A	0046982	molecular_function	protein heterodimerization activity
A	0070062	cellular_component	extracellular exosome
B	0000781	cellular_component	chromosome, telomeric region
B	0000786	cellular_component	nucleosome
B	0003677	molecular_function	DNA binding
B	0003723	molecular_function	RNA binding
B	0005515	molecular_function	protein binding
B	0005576	cellular_component	extracellular region
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005694	cellular_component	chromosome
B	0006325	biological_process	chromatin organization
B	0006334	biological_process	nucleosome assembly
B	0016020	cellular_component	membrane
B	0030527	molecular_function	structural constituent of chromatin
B	0032200	biological_process	telomere organization
B	0032991	cellular_component	protein-containing complex
B	0043505	cellular_component	CENP-A containing nucleosome
B	0045653	biological_process	negative regulation of megakaryocyte differentiation
B	0046982	molecular_function	protein heterodimerization activity
B	0061644	biological_process	protein localization to CENP-A containing chromatin
B	0070062	cellular_component	extracellular exosome
C	0000786	cellular_component	nucleosome
C	0003677	molecular_function	DNA binding
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005694	cellular_component	chromosome
C	0006325	biological_process	chromatin organization
C	0008285	biological_process	negative regulation of cell population proliferation
C	0030527	molecular_function	structural constituent of chromatin
C	0031492	molecular_function	nucleosomal DNA binding
C	0031507	biological_process	heterochromatin formation
C	0043229	cellular_component	intracellular organelle
C	0043505	cellular_component	CENP-A containing nucleosome
C	0046982	molecular_function	protein heterodimerization activity
C	0061644	biological_process	protein localization to CENP-A containing chromatin
C	0070062	cellular_component	extracellular exosome
D	0000786	cellular_component	nucleosome
D	0001530	molecular_function	lipopolysaccharide binding
D	0002227	biological_process	innate immune response in mucosa
D	0003677	molecular_function	DNA binding
D	0005515	molecular_function	protein binding
D	0005615	cellular_component	extracellular space
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005694	cellular_component	chromosome
D	0005829	cellular_component	cytosol
D	0005886	cellular_component	plasma membrane
D	0006325	biological_process	chromatin organization
D	0006334	biological_process	nucleosome assembly
D	0010804	biological_process	negative regulation of tumor necrosis factor-mediated signaling pathway
D	0019731	biological_process	antibacterial humoral response
D	0030527	molecular_function	structural constituent of chromatin
D	0031640	biological_process	killing of cells of another organism
D	0042742	biological_process	defense response to bacterium
D	0043229	cellular_component	intracellular organelle
D	0043505	cellular_component	CENP-A containing nucleosome
D	0046982	molecular_function	protein heterodimerization activity
D	0050829	biological_process	defense response to Gram-negative bacterium
D	0050830	biological_process	defense response to Gram-positive bacterium
D	0061644	biological_process	protein localization to CENP-A containing chromatin
D	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
E	0000786	cellular_component	nucleosome
E	0003677	molecular_function	DNA binding
E	0005515	molecular_function	protein binding
E	0005576	cellular_component	extracellular region
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005694	cellular_component	chromosome
E	0006325	biological_process	chromatin organization
E	0006334	biological_process	nucleosome assembly
E	0010467	biological_process	gene expression
E	0016020	cellular_component	membrane
E	0030527	molecular_function	structural constituent of chromatin
E	0032200	biological_process	telomere organization
E	0032991	cellular_component	protein-containing complex
E	0040029	biological_process	epigenetic regulation of gene expression
E	0043229	cellular_component	intracellular organelle
E	0045296	molecular_function	cadherin binding
E	0046982	molecular_function	protein heterodimerization activity
E	0070062	cellular_component	extracellular exosome
F	0000781	cellular_component	chromosome, telomeric region
F	0000786	cellular_component	nucleosome
F	0003677	molecular_function	DNA binding
F	0003723	molecular_function	RNA binding
F	0005515	molecular_function	protein binding
F	0005576	cellular_component	extracellular region
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005694	cellular_component	chromosome
F	0006325	biological_process	chromatin organization
F	0006334	biological_process	nucleosome assembly
F	0016020	cellular_component	membrane
F	0030527	molecular_function	structural constituent of chromatin
F	0032200	biological_process	telomere organization
F	0032991	cellular_component	protein-containing complex
F	0043505	cellular_component	CENP-A containing nucleosome
F	0045653	biological_process	negative regulation of megakaryocyte differentiation
F	0046982	molecular_function	protein heterodimerization activity
F	0061644	biological_process	protein localization to CENP-A containing chromatin
F	0070062	cellular_component	extracellular exosome
G	0000786	cellular_component	nucleosome
G	0003677	molecular_function	DNA binding
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005694	cellular_component	chromosome
G	0006325	biological_process	chromatin organization
G	0008285	biological_process	negative regulation of cell population proliferation
G	0030527	molecular_function	structural constituent of chromatin
G	0031492	molecular_function	nucleosomal DNA binding
G	0031507	biological_process	heterochromatin formation
G	0043229	cellular_component	intracellular organelle
G	0043505	cellular_component	CENP-A containing nucleosome
G	0046982	molecular_function	protein heterodimerization activity
G	0061644	biological_process	protein localization to CENP-A containing chromatin
G	0070062	cellular_component	extracellular exosome
H	0000786	cellular_component	nucleosome
H	0001530	molecular_function	lipopolysaccharide binding
H	0002227	biological_process	innate immune response in mucosa
H	0003677	molecular_function	DNA binding
H	0005515	molecular_function	protein binding
H	0005615	cellular_component	extracellular space
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0005694	cellular_component	chromosome
H	0005829	cellular_component	cytosol
H	0005886	cellular_component	plasma membrane
H	0006325	biological_process	chromatin organization
H	0006334	biological_process	nucleosome assembly
H	0010804	biological_process	negative regulation of tumor necrosis factor-mediated signaling pathway
H	0019731	biological_process	antibacterial humoral response
H	0030527	molecular_function	structural constituent of chromatin
H	0031640	biological_process	killing of cells of another organism
H	0042742	biological_process	defense response to bacterium
H	0043229	cellular_component	intracellular organelle
H	0043505	cellular_component	CENP-A containing nucleosome
H	0046982	molecular_function	protein heterodimerization activity
H	0050829	biological_process	defense response to Gram-negative bacterium
H	0050830	biological_process	defense response to Gram-positive bacterium
H	0061644	biological_process	protein localization to CENP-A containing chromatin
H	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
K	0000122	biological_process	negative regulation of transcription by RNA polymerase II
K	0000976	molecular_function	transcription cis-regulatory region binding
K	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
K	0000981	molecular_function	DNA-binding transcription factor activity, RNA polymerase II-specific
K	0001227	molecular_function	DNA-binding transcription repressor activity, RNA polymerase II-specific
K	0001714	biological_process	endodermal cell fate specification
K	0001824	biological_process	blastocyst development
K	0003674	molecular_function	molecular_function
K	0003677	molecular_function	DNA binding
K	0003700	molecular_function	DNA-binding transcription factor activity
K	0003723	molecular_function	RNA binding
K	0005515	molecular_function	protein binding
K	0005575	cellular_component	cellular_component
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005737	cellular_component	cytoplasm
K	0005739	cellular_component	mitochondrion
K	0005829	cellular_component	cytosol
K	0006091	biological_process	generation of precursor metabolites and energy
K	0006355	biological_process	regulation of DNA-templated transcription
K	0006357	biological_process	regulation of transcription by RNA polymerase II
K	0008218	biological_process	bioluminescence
K	0009611	biological_process	response to wounding
K	0009653	biological_process	anatomical structure morphogenesis
K	0009786	biological_process	regulation of asymmetric cell division
K	0010468	biological_process	regulation of gene expression
K	0031625	molecular_function	ubiquitin protein ligase binding
K	0035019	biological_process	somatic stem cell population maintenance
K	0035198	molecular_function	miRNA binding
K	0043565	molecular_function	sequence-specific DNA binding
K	0045944	biological_process	positive regulation of transcription by RNA polymerase II
K	1902894	biological_process	negative regulation of miRNA transcription
K	1990837	molecular_function	sequence-specific double-stranded DNA binding

Functional Information from PDB Data

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

Chain	Residue
A	LYS116
E	LYS123

---

site_id	AC2
Number of Residues	2
Details	binding site for residue PTD A 202

Chain	Residue
A	LYS123
E	LYS116

---

site_id	AC3
Number of Residues	2
Details	binding site for residue PTD B 201

Chain	Residue
A	LYS80
B	LYS80

---

site_id	AC4
Number of Residues	2
Details	binding site for residue PTD C 301

Chain	Residue
C	LYS37
H	LYS86

---

site_id	AC5
Number of Residues	2
Details	binding site for residue PTD D 201

Chain	Residue
D	LYS47
D	LYS44

---

site_id	AC6
Number of Residues	2
Details	binding site for residue PTD D 202

Chain	Residue
D	LYS86
G	LYS37

---

site_id	AC7
Number of Residues	2
Details	binding site for residue PTD F 201

Chain	Residue
E	LYS80
F	LYS80

---

site_id	AC8
Number of Residues	2
Details	binding site for residue PTD H 201

Chain	Residue
H	LYS44
H	LYS47

---

Functional Information from PROSITE/UniProt

site_id	PS00027
Number of Residues	24
Details	HOMEOBOX_1 'Homeobox' domain signature. IAqqLgLEkdVVRVWFcNrrqkgK

Chain	Residue	Details
K	ILE263-LYS286

---

site_id	PS00035
Number of Residues	13
Details	POU_1 POU-specific (POUs) domain signature 1. KRItLGYtQaDVG

Chain	Residue	Details
K	LYS156-GLY168

---

site_id	PS00046
Number of Residues	7
Details	HISTONE_H2A Histone H2A signature. AGLqFPV

Chain	Residue	Details
C	ALA22-VAL28

---

site_id	PS00047
Number of Residues	5
Details	HISTONE_H4 Histone H4 signature. GAKRH

Chain	Residue	Details
F	GLY15-HIS19
B	GLY16-HIS20

---

site_id	PS00322
Number of Residues	7
Details	HISTONE_H3_1 Histone H3 signature 1. KAPRKQL

Chain	Residue	Details
E	LYS15-LEU21
A	LYS15-LEU21

---

site_id	PS00357
Number of Residues	23
Details	HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG

Chain	Residue	Details
D	ARG93-GLY115

---

site_id	PS00465
Number of Residues	14
Details	POU_2 POU-specific (POUs) domain signature 2. SQTTICRFEaLqLS

Chain	Residue	Details
K	SER180-SER193

---

site_id	PS00959
Number of Residues	9
Details	HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI

Chain	Residue	Details
E	PRO67-ILE75
A	PRO67-ILE75

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	68
Details	DNA_BIND: HMG box => ECO:0000255|PROSITE-ProRule:PRU00267

Chain	Residue	Details
L	VAL41-LYS109
H	PRO2

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: N6-methyllysine => ECO:0000269|PubMed:29358331

Chain	Residue	Details
L	LYS42
L	LYS117

---

site_id	SWS_FT_FI3
Number of Residues	59
Details	DNA_BIND: Homeobox => ECO:0000255|PROSITE-ProRule:PRU00108

Chain	Residue	Details
K	ARG230-SER289
H	LYS12
H	LYS16
H	LYS17
H	LYS21
H	LYS24
H	LYS44
H	LYS86
D	LYS12
D	LYS16
D	LYS17
D	LYS21
D	LYS24
D	LYS44
D	LYS86
H	LYS6

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	BINDING: BINDING => ECO:0000250|UniProtKB:P20263

Chain	Residue	Details
K	ARG157
K	GLN164
G	LYS10
G	LYS96

---

site_id	SWS_FT_FI5
Number of Residues	1
Details	MOD_RES: Phosphoserine; by MAPK => ECO:0000269|PubMed:22474382, ECO:0000269|PubMed:23024368

Chain	Residue	Details
K	SER111
F	LYS17
F	LYS45

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0000269|PubMed:22474382

Chain	Residue	Details
K	THR235
F	LYS32
F	LYS78
F	LYS92

---

site_id	SWS_FT_FI7
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:22474382

Chain	Residue	Details
K	SER236
K	SER289
K	SER290
K	SER355

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) => ECO:0000250|UniProtKB:P20263

Chain	Residue	Details
K	LYS123
D	LYS117
D	LYS121
H	LYS35
H	LYS117
H	LYS121

---

site_id	SWS_FT_FI9
Number of Residues	1
Details	MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:15592455, ECO:0007744|PubMed:20068231

Chain	Residue	Details
F	TYR52
H	GLU36
C	LYS126
G	LYS119
G	LYS120
G	LYS126

---

site_id	SWS_FT_FI10
Number of Residues	1
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297

Chain	Residue	Details
F	LYS60
E	LYS57

---

site_id	SWS_FT_FI11
Number of Residues	1
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P62806

Chain	Residue	Details
F	LYS80
D	LYS109
H	LYS47
H	LYS109

---

site_id	SWS_FT_FI12
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P62806

Chain	Residue	Details
F	THR81
E	LYS65
G	LYS120

---

site_id	SWS_FT_FI13
Number of Residues	1
Details	MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:24275569

Chain	Residue	Details
F	TYR89
H	ARG80

---

site_id	SWS_FT_FI14
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:25218447

Chain	Residue	Details
F	LYS13
D	ARG93
H	ARG87
H	ARG93

---

site_id	SWS_FT_FI15
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:19818714

Chain	Residue	Details
E	LYS28
F	LYS92

---

site_id	SWS_FT_FI16
Number of Residues	3
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:28112733

Chain	Residue	Details
F	LYS21
F	LYS60
F	LYS80

---

site_id	SWS_FT_FI17
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate => ECO:0000269|PubMed:30886146

Chain	Residue	Details
F	LYS32
H	LYS6

---

site_id	SWS_FT_FI18
Number of Residues	1
Details	MOD_RES: N6-methyllysine => ECO:0000269|PubMed:15983376

Chain	Residue	Details
E	LYS38
D	LYS121
H	LYS121

---

site_id	SWS_FT_FI19
Number of Residues	1
Details	MOD_RES: Phosphotyrosine => ECO:0000269|PubMed:19783980

Chain	Residue	Details
E	TYR42
H	LYS21

---

site_id	SWS_FT_FI20
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:20850016

Chain	Residue	Details
E	SER58
H	LYS35

---

site_id	SWS_FT_FI21
Number of Residues	1
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:29211711

Chain	Residue	Details
E	LYS80

---

site_id	SWS_FT_FI22
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0000269|PubMed:20850016

Chain	Residue	Details
E	THR81

---

site_id	SWS_FT_FI23
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243

Chain	Residue	Details
E	SER87

---

site_id	SWS_FT_FI24
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3

Chain	Residue	Details
E	THR108

---

site_id	SWS_FT_FI25
Number of Residues	1
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297

Chain	Residue	Details
E	LYS116

---

site_id	SWS_FT_FI26
Number of Residues	1
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:27436229

Chain	Residue	Details
E	LYS123

---

site_id	SWS_FT_FI27
Number of Residues	1
Details	LIPID: N6-decanoyllysine => ECO:0000269|PubMed:35939806

Chain	Residue	Details
E	LYS19

---