Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

9EOZ

Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
A	0003677	molecular_function	DNA binding
A	0003684	molecular_function	damaged DNA binding
A	0003824	molecular_function	catalytic activity
A	0004519	molecular_function	endonuclease activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005739	cellular_component	mitochondrion
A	0005759	cellular_component	mitochondrial matrix
A	0005829	cellular_component	cytosol
A	0006281	biological_process	DNA repair
A	0006284	biological_process	base-excision repair
A	0006285	biological_process	base-excision repair, AP site formation
A	0006289	biological_process	nucleotide-excision repair
A	0006355	biological_process	regulation of DNA-templated transcription
A	0006974	biological_process	DNA damage response
A	0006979	biological_process	response to oxidative stress
A	0008017	molecular_function	microtubule binding
A	0008534	molecular_function	oxidized purine nucleobase lesion DNA N-glycosylase activity
A	0009314	biological_process	response to radiation
A	0016363	cellular_component	nuclear matrix
A	0016607	cellular_component	nuclear speck
A	0016787	molecular_function	hydrolase activity
A	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
A	0016829	molecular_function	lyase activity
A	0019899	molecular_function	enzyme binding
A	0032357	molecular_function	oxidized purine DNA binding
A	0032991	cellular_component	protein-containing complex
A	0034039	molecular_function	8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
A	0034614	biological_process	cellular response to reactive oxygen species
A	0044029	biological_process	positive regulation of gene expression via chromosomal CpG island demethylation
A	0045007	biological_process	depurination
A	0045008	biological_process	depyrimidination
A	0045944	biological_process	positive regulation of transcription by RNA polymerase II
A	0140078	molecular_function	class I DNA-(apurinic or apyrimidinic site) endonuclease activity
A	1901291	biological_process	negative regulation of double-strand break repair via single-strand annealing
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
E	0000775	cellular_component	chromosome, centromeric region
E	0000781	cellular_component	chromosome, telomeric region
E	0000785	cellular_component	chromatin
E	0000786	cellular_component	nucleosome
E	0000939	cellular_component	inner kinetochore
E	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
E	0000979	molecular_function	RNA polymerase II core promoter sequence-specific DNA binding
E	0001556	biological_process	oocyte maturation
E	0001649	biological_process	osteoblast differentiation
E	0001740	cellular_component	Barr body
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	0006334	biological_process	nucleosome assembly
E	0006997	biological_process	nucleus organization
E	0007283	biological_process	spermatogenesis
E	0007286	biological_process	spermatid development
E	0007338	biological_process	single fertilization
E	0007566	biological_process	embryo implantation
E	0008283	biological_process	cell population proliferation
E	0008584	biological_process	male gonad development
E	0030307	biological_process	positive regulation of cell growth
E	0030527	molecular_function	structural constituent of chromatin
E	0031492	molecular_function	nucleosomal DNA binding
E	0031508	biological_process	pericentric heterochromatin formation
E	0031509	biological_process	subtelomeric heterochromatin formation
E	0032200	biological_process	telomere organization
E	0032991	cellular_component	protein-containing complex
E	0035264	biological_process	multicellular organism growth
E	0042692	biological_process	muscle cell differentiation
E	0046982	molecular_function	protein heterodimerization activity
E	0048477	biological_process	oogenesis
E	0070062	cellular_component	extracellular exosome
E	0090230	biological_process	regulation of centromere complex assembly
E	1902340	biological_process	negative regulation of chromosome condensation
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	0005654	cellular_component	nucleoplasm
G	0005694	cellular_component	chromosome
G	0008285	biological_process	negative regulation of cell population proliferation
G	0030527	molecular_function	structural constituent of chromatin
G	0031507	biological_process	heterochromatin formation
G	0046982	molecular_function	protein heterodimerization activity
G	0070062	cellular_component	extracellular exosome
H	0000786	cellular_component	nucleosome
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	0006334	biological_process	nucleosome assembly
H	0019731	biological_process	antibacterial humoral response
H	0030527	molecular_function	structural constituent of chromatin
H	0042742	biological_process	defense response to bacterium
H	0042802	molecular_function	identical protein binding
H	0046982	molecular_function	protein heterodimerization activity
H	0050830	biological_process	defense response to Gram-positive bacterium
H	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
H	0070062	cellular_component	extracellular exosome
K	0000775	cellular_component	chromosome, centromeric region
K	0000781	cellular_component	chromosome, telomeric region
K	0000785	cellular_component	chromatin
K	0000786	cellular_component	nucleosome
K	0000939	cellular_component	inner kinetochore
K	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
K	0000979	molecular_function	RNA polymerase II core promoter sequence-specific DNA binding
K	0001556	biological_process	oocyte maturation
K	0001649	biological_process	osteoblast differentiation
K	0001740	cellular_component	Barr body
K	0003677	molecular_function	DNA binding
K	0005515	molecular_function	protein binding
K	0005576	cellular_component	extracellular region
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005694	cellular_component	chromosome
K	0006334	biological_process	nucleosome assembly
K	0006997	biological_process	nucleus organization
K	0007283	biological_process	spermatogenesis
K	0007286	biological_process	spermatid development
K	0007338	biological_process	single fertilization
K	0007566	biological_process	embryo implantation
K	0008283	biological_process	cell population proliferation
K	0008584	biological_process	male gonad development
K	0030307	biological_process	positive regulation of cell growth
K	0030527	molecular_function	structural constituent of chromatin
K	0031492	molecular_function	nucleosomal DNA binding
K	0031508	biological_process	pericentric heterochromatin formation
K	0031509	biological_process	subtelomeric heterochromatin formation
K	0032200	biological_process	telomere organization
K	0032991	cellular_component	protein-containing complex
K	0035264	biological_process	multicellular organism growth
K	0042692	biological_process	muscle cell differentiation
K	0046982	molecular_function	protein heterodimerization activity
K	0048477	biological_process	oogenesis
K	0070062	cellular_component	extracellular exosome
K	0090230	biological_process	regulation of centromere complex assembly
K	1902340	biological_process	negative regulation of chromosome condensation
L	0000786	cellular_component	nucleosome
L	0003677	molecular_function	DNA binding
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
L	0005654	cellular_component	nucleoplasm
L	0005694	cellular_component	chromosome
L	0008285	biological_process	negative regulation of cell population proliferation
L	0030527	molecular_function	structural constituent of chromatin
L	0031507	biological_process	heterochromatin formation
L	0046982	molecular_function	protein heterodimerization activity
L	0070062	cellular_component	extracellular exosome
M	0000786	cellular_component	nucleosome
M	0002227	biological_process	innate immune response in mucosa
M	0003677	molecular_function	DNA binding
M	0005515	molecular_function	protein binding
M	0005615	cellular_component	extracellular space
M	0005634	cellular_component	nucleus
M	0005654	cellular_component	nucleoplasm
M	0005694	cellular_component	chromosome
M	0005829	cellular_component	cytosol
M	0006334	biological_process	nucleosome assembly
M	0019731	biological_process	antibacterial humoral response
M	0030527	molecular_function	structural constituent of chromatin
M	0042742	biological_process	defense response to bacterium
M	0042802	molecular_function	identical protein binding
M	0046982	molecular_function	protein heterodimerization activity
M	0050830	biological_process	defense response to Gram-positive bacterium
M	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
M	0070062	cellular_component	extracellular exosome

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
G	ALA21-VAL27

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

Chain	Residue	Details
B	GLY14-HIS18

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

Chain	Residue	Details
E	LYS14-LEU20

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

Chain	Residue	Details
H	ARG89-GLY111

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

Chain	Residue	Details
E	PRO66-ILE74

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	Active site: {"description":"Schiff-base intermediate with DNA","evidences":[{"source":"PubMed","id":"9197244","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10706276","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11902834","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12578369","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12592398","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15610848","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Binding site: {}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	1
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"12086618","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15964846","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17967882","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27338793","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	16
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Modified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"PubMed","id":"17267393","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine; by PAK2","evidences":[{"source":"PubMed","id":"21724829","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17081983","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"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_FI8
Number of Residues	2
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"15592455","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	6
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"PubMed","id":"31542297","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62806","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P62806","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	2
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	5
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

site_id	SWS_FT_FI14
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"PubMed","id":"19818714","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate","evidences":[{"source":"PubMed","id":"30886146","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	2
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"19783980","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"20850016","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	2
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"16267050","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17194708","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"29211711","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"20850016","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI23
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27436229","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI24
Number of Residues	2
Details	Modified residue: {"description":"N6-crotonyllysine; alternate","evidences":[{"source":"PubMed","id":"21925322","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI25
Number of Residues	4
Details	Modified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine","evidences":[{"source":"PubMed","id":"24681537","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI26
Number of Residues	2
Details	Modified residue: {"description":"N5-methylglutamine","evidences":[{"source":"PubMed","id":"24352239","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI27
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22713238","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22980979","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI28
Number of Residues	2
Details	Modified residue: {"description":"PolyADP-ribosyl glutamic acid","evidences":[{"source":"UniProtKB","id":"Q64475","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI29
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine; by AMPK","evidences":[{"source":"UniProtKB","id":"Q6ZWY9","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI30
Number of Residues	4
Details	Modified residue: {"description":"N6-lactoyllysine; alternate","evidences":[{"source":"PubMed","id":"31645732","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI31
Number of Residues	4
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"16627869","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI32
Number of Residues	2
Details	Modified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine; alternate","evidences":[{"source":"PubMed","id":"24681537","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI33
Number of Residues	2
Details	Modified residue: {"description":"Dimethylated arginine","evidences":[{"source":"UniProtKB","id":"Q96A08","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI34
Number of Residues	4
Details	Modified residue: {"description":"Omega-N-methylarginine","evidences":[{"source":"UniProtKB","id":"Q96A08","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI35
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q00729","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI36
Number of Residues	2
Details	Glycosylation: {"description":"O-linked (GlcNAc) serine","evidences":[{"source":"PubMed","id":"22121020","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI37
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"PubMed","id":"21726816","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI38
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"PubMed","id":"16307923","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16627869","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16713563","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22121020","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	2
Details	M-CSA 185

Chain	Residue	Details
A	GLN249	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
A	ASP268	electrostatic stabiliser, hydrogen bond acceptor

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)