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7U50

APE1 bound to a nucleosome core particle with AP-site at SHL-6

Functional Information from GO Data
ChainGOidnamespacecontents
A0000786cellular_componentnucleosome
A0003677molecular_functionDNA binding
A0005515molecular_functionprotein binding
A0005576cellular_componentextracellular region
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005694cellular_componentchromosome
A0006325biological_processchromatin organization
A0006334biological_processnucleosome assembly
A0030527molecular_functionstructural constituent of chromatin
A0043229cellular_componentintracellular organelle
A0046982molecular_functionprotein heterodimerization activity
A0070062cellular_componentextracellular exosome
B0000781cellular_componentchromosome, telomeric region
B0000786cellular_componentnucleosome
B0003677molecular_functionDNA binding
B0003723molecular_functionRNA binding
B0005515molecular_functionprotein binding
B0005576cellular_componentextracellular region
B0005634cellular_componentnucleus
B0005654cellular_componentnucleoplasm
B0005694cellular_componentchromosome
B0006325biological_processchromatin organization
B0006334biological_processnucleosome assembly
B0016020cellular_componentmembrane
B0030527molecular_functionstructural constituent of chromatin
B0032200biological_processtelomere organization
B0032991cellular_componentprotein-containing complex
B0043505cellular_componentCENP-A containing nucleosome
B0045653biological_processnegative regulation of megakaryocyte differentiation
B0046982molecular_functionprotein heterodimerization activity
B0061644biological_processprotein localization to CENP-A containing chromatin
B0070062cellular_componentextracellular exosome
C0000786cellular_componentnucleosome
C0003677molecular_functionDNA binding
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005694cellular_componentchromosome
C0008150biological_processbiological_process
C0019899molecular_functionenzyme binding
C0030527molecular_functionstructural constituent of chromatin
C0031492molecular_functionnucleosomal DNA binding
C0031507biological_processheterochromatin formation
C0043229cellular_componentintracellular organelle
C0046982molecular_functionprotein heterodimerization activity
C0070062cellular_componentextracellular exosome
D0000786cellular_componentnucleosome
D0002227biological_processinnate immune response in mucosa
D0003677molecular_functionDNA binding
D0005515molecular_functionprotein binding
D0005615cellular_componentextracellular space
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0005694cellular_componentchromosome
D0005829cellular_componentcytosol
D0006334biological_processnucleosome assembly
D0019731biological_processantibacterial humoral response
D0030527molecular_functionstructural constituent of chromatin
D0042742biological_processdefense response to bacterium
D0042802molecular_functionidentical protein binding
D0043229cellular_componentintracellular organelle
D0046982molecular_functionprotein heterodimerization activity
D0050830biological_processdefense response to Gram-positive bacterium
D0061844biological_processantimicrobial humoral immune response mediated by antimicrobial peptide
D0070062cellular_componentextracellular exosome
E0000786cellular_componentnucleosome
E0003677molecular_functionDNA binding
E0005515molecular_functionprotein binding
E0005576cellular_componentextracellular region
E0005634cellular_componentnucleus
E0005654cellular_componentnucleoplasm
E0005694cellular_componentchromosome
E0006325biological_processchromatin organization
E0006334biological_processnucleosome assembly
E0030527molecular_functionstructural constituent of chromatin
E0043229cellular_componentintracellular organelle
E0046982molecular_functionprotein heterodimerization activity
E0070062cellular_componentextracellular exosome
F0000781cellular_componentchromosome, telomeric region
F0000786cellular_componentnucleosome
F0003677molecular_functionDNA binding
F0003723molecular_functionRNA binding
F0005515molecular_functionprotein binding
F0005576cellular_componentextracellular region
F0005634cellular_componentnucleus
F0005654cellular_componentnucleoplasm
F0005694cellular_componentchromosome
F0006325biological_processchromatin organization
F0006334biological_processnucleosome assembly
F0016020cellular_componentmembrane
F0030527molecular_functionstructural constituent of chromatin
F0032200biological_processtelomere organization
F0032991cellular_componentprotein-containing complex
F0043505cellular_componentCENP-A containing nucleosome
F0045653biological_processnegative regulation of megakaryocyte differentiation
F0046982molecular_functionprotein heterodimerization activity
F0061644biological_processprotein localization to CENP-A containing chromatin
F0070062cellular_componentextracellular exosome
G0000786cellular_componentnucleosome
G0003677molecular_functionDNA binding
G0005515molecular_functionprotein binding
G0005634cellular_componentnucleus
G0005694cellular_componentchromosome
G0008150biological_processbiological_process
G0019899molecular_functionenzyme binding
G0030527molecular_functionstructural constituent of chromatin
G0031492molecular_functionnucleosomal DNA binding
G0031507biological_processheterochromatin formation
G0043229cellular_componentintracellular organelle
G0046982molecular_functionprotein heterodimerization activity
G0070062cellular_componentextracellular exosome
H0000786cellular_componentnucleosome
H0002227biological_processinnate immune response in mucosa
H0003677molecular_functionDNA binding
H0005515molecular_functionprotein binding
H0005615cellular_componentextracellular space
H0005634cellular_componentnucleus
H0005654cellular_componentnucleoplasm
H0005694cellular_componentchromosome
H0005829cellular_componentcytosol
H0006334biological_processnucleosome assembly
H0019731biological_processantibacterial humoral response
H0030527molecular_functionstructural constituent of chromatin
H0042742biological_processdefense response to bacterium
H0042802molecular_functionidentical protein binding
H0043229cellular_componentintracellular organelle
H0046982molecular_functionprotein heterodimerization activity
H0050830biological_processdefense response to Gram-positive bacterium
H0061844biological_processantimicrobial humoral immune response mediated by antimicrobial peptide
H0070062cellular_componentextracellular exosome
K0000723biological_processtelomere maintenance
K0000781cellular_componentchromosome, telomeric region
K0003677molecular_functionDNA binding
K0003684molecular_functiondamaged DNA binding
K0003691molecular_functiondouble-stranded telomeric DNA binding
K0003713molecular_functiontranscription coactivator activity
K0003714molecular_functiontranscription corepressor activity
K0003723molecular_functionRNA binding
K0003824molecular_functioncatalytic activity
K0003906molecular_functionDNA-(apurinic or apyrimidinic site) endonuclease activity
K0004518molecular_functionnuclease activity
K0004519molecular_functionendonuclease activity
K0004520molecular_functionDNA endonuclease activity
K0004523molecular_functionRNA-DNA hybrid ribonuclease activity
K0004527molecular_functionexonuclease activity
K0004528molecular_functionphosphodiesterase I activity
K0004844molecular_functionuracil DNA N-glycosylase activity
K0005515molecular_functionprotein binding
K0005634cellular_componentnucleus
K0005654cellular_componentnucleoplasm
K0005730cellular_componentnucleolus
K0005737cellular_componentcytoplasm
K0005739cellular_componentmitochondrion
K0005783cellular_componentendoplasmic reticulum
K0005813cellular_componentcentrosome
K0005840cellular_componentribosome
K0006281biological_processDNA repair
K0006284biological_processbase-excision repair
K0006287biological_processbase-excision repair, gap-filling
K0006308biological_processDNA catabolic process
K0006310biological_processDNA recombination
K0008081molecular_functionphosphoric diester hydrolase activity
K0008296molecular_function3'-5'-DNA exonuclease activity
K0008309molecular_functiondouble-stranded DNA exodeoxyribonuclease activity
K0008311molecular_functiondouble-stranded DNA 3'-5' DNA exonuclease activity
K0008408molecular_function3'-5' exonuclease activity
K0016491molecular_functionoxidoreductase activity
K0016607cellular_componentnuclear speck
K0016890molecular_functionsite-specific endodeoxyribonuclease activity, specific for altered base
K0031490molecular_functionchromatin DNA binding
K0042981biological_processregulation of apoptotic process
K0043488biological_processregulation of mRNA stability
K0044029biological_processpositive regulation of gene expression via chromosomal CpG island demethylation
K0045454biological_processcell redox homeostasis
K0045892biological_processnegative regulation of DNA-templated transcription
K0045944biological_processpositive regulation of transcription by RNA polymerase II
K0046872molecular_functionmetal ion binding
K0048471cellular_componentperinuclear region of cytoplasm
K0052720molecular_functionclass II DNA-(apurinic or apyrimidinic site) endonuclease activity
K0090580molecular_functionphosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands
K0097698biological_processtelomere maintenance via base-excision repair
K0140431molecular_functionDNA-(abasic site) binding
Functional Information from PROSITE/UniProt
site_idPS00046
Number of Residues7
DetailsHISTONE_H2A Histone H2A signature. AGLqFPV
ChainResidueDetails
CALA21-VAL27

site_idPS00047
Number of Residues5
DetailsHISTONE_H4 Histone H4 signature. GAKRH
ChainResidueDetails
BGLY14-HIS18

site_idPS00322
Number of Residues7
DetailsHISTONE_H3_1 Histone H3 signature 1. KAPRKQL
ChainResidueDetails
ALYS14-LEU20

site_idPS00357
Number of Residues23
DetailsHISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG
ChainResidueDetails
DARG92-GLY114

site_idPS00726
Number of Residues10
DetailsAP_NUCLEASE_F1_1 AP endonucleases family 1 signature 1. PDILCLQETK
ChainResidueDetails
KPRO89-LYS98

site_idPS00727
Number of Residues17
DetailsAP_NUCLEASE_F1_2 AP endonucleases family 1 signature 2. DSFRHlypntpyaYTFW
ChainResidueDetails
KASP251-TRP267

site_idPS00728
Number of Residues12
DetailsAP_NUCLEASE_F1_3 AP endonucleases family 1 signature 3. NvGwRLDYfLlS
ChainResidueDetails
KASN277-SER288

site_idPS00959
Number of Residues9
DetailsHISTONE_H3_2 Histone H3 signature 2. PFqRLVREI
ChainResidueDetails
APRO66-ILE74

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsACT_SITE: ACT_SITE => ECO:0000269|PubMed:15380100
ChainResidueDetails
KTYR171
HPRO1

site_idSWS_FT_FI2
Number of Residues1
DetailsACT_SITE: Proton donor/acceptor => ECO:0000269|PubMed:9351835, ECO:0007744|PDB:1BIX
ChainResidueDetails
KASP210
HGLU2

site_idSWS_FT_FI3
Number of Residues1
DetailsACT_SITE: Proton acceptor => ECO:0000255|PROSITE-ProRule:PRU00764
ChainResidueDetails
KHIS309
HLYS11
HLYS15
HLYS16
HLYS20
HLYS23
HLYS43
HLYS85
DLYS11
DLYS15
DLYS16
DLYS20
DLYS23
DLYS43
DLYS85
HLYS5

site_idSWS_FT_FI4
Number of Residues6
DetailsBINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00764
ChainResidueDetails
KASN68
KGLU96
KASP210
KASN212
KASP308
KHIS309

site_idSWS_FT_FI5
Number of Residues1
DetailsSITE: Cleavage; by granzyme A
ChainResidueDetails
KLYS31
HLYS12
BLYS44
FLYS8
FLYS16
FLYS44

site_idSWS_FT_FI6
Number of Residues1
DetailsSITE: Transition state stabilizer => ECO:0000269|PubMed:8932375
ChainResidueDetails
KASN212
HSER14
BLYS77
BLYS91
FLYS12
FLYS31
FLYS77
FLYS91

site_idSWS_FT_FI7
Number of Residues1
DetailsSITE: Important for catalytic activity => ECO:0000269|PubMed:21762700, ECO:0000269|PubMed:9804799
ChainResidueDetails
KASP283
HLYS24

site_idSWS_FT_FI8
Number of Residues1
DetailsSITE: Interaction with DNA substrate
ChainResidueDetails
KHIS309
DLYS116
DLYS120
HLYS34
HLYS116
HLYS120

site_idSWS_FT_FI9
Number of Residues2
DetailsMOD_RES: N6-acetyllysine; by EP300 => ECO:0000269|PubMed:14633989
ChainResidueDetails
KLYS6
KLYS7
CLYS125
GLYS118
GLYS119
GLYS125

site_idSWS_FT_FI10
Number of Residues4
DetailsMOD_RES: N6-acetyllysine => ECO:0000269|PubMed:20699270
ChainResidueDetails
KLYS27
KLYS31
KLYS32
KLYS35

site_idSWS_FT_FI11
Number of Residues1
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163
ChainResidueDetails
KSER54
DLYS108
HLYS46
HLYS108

site_idSWS_FT_FI12
Number of Residues2
DetailsMOD_RES: S-nitrosocysteine; alternate => ECO:0000269|PubMed:17403694
ChainResidueDetails
KCYS65
KCYS93
GLYS119

site_idSWS_FT_FI13
Number of Residues1
DetailsMOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861
ChainResidueDetails
KLYS197
HARG79

site_idSWS_FT_FI14
Number of Residues1
DetailsMOD_RES: Phosphothreonine; by CDK5 => ECO:0000250|UniProtKB:P28352
ChainResidueDetails
KTHR233
DARG92
HARG86
HARG92

site_idSWS_FT_FI15
Number of Residues1
DetailsMOD_RES: S-nitrosocysteine => ECO:0000269|PubMed:17403694
ChainResidueDetails
KCYS310
HTHR115
FLYS91

site_idSWS_FT_FI16
Number of Residues2
DetailsCARBOHYD: O-linked (GlcNAc) serine => ECO:0000269|PubMed:22121020
ChainResidueDetails
DSER112
HSER112
BLYS79
FLYS20
FLYS59
FLYS79

site_idSWS_FT_FI17
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0000250|UniProtKB:P58876
ChainResidueDetails
DLYS5
HLYS5

site_idSWS_FT_FI18
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:16307923, ECO:0000269|PubMed:16627869, ECO:0000269|PubMed:16713563, ECO:0000269|PubMed:22121020
ChainResidueDetails
ASER57
DLYS120
HLYS120

site_idSWS_FT_FI19
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0000250|UniProtKB:Q5QNW6
ChainResidueDetails
DLYS20
HLYS20

site_idSWS_FT_FI20
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:21726816
ChainResidueDetails
DLYS34
HLYS34

site_idSWS_FT_FI21
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243
ChainResidueDetails
ASER86
ESER86

site_idSWS_FT_FI22
Number of Residues2
DetailsMOD_RES: Phosphothreonine => ECO:0007744|PubMed:19690332
ChainResidueDetails
ATHR107
ETHR107

site_idSWS_FT_FI23
Number of Residues2
DetailsMOD_RES: N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297
ChainResidueDetails
ALYS115
ELYS115

site_idSWS_FT_FI24
Number of Residues2
DetailsMOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:27436229
ChainResidueDetails
ALYS122
ELYS122

site_idSWS_FT_FI25
Number of Residues2
DetailsLIPID: N6-decanoyllysine => ECO:0000269|PubMed:35939806
ChainResidueDetails
ALYS18
ELYS18

site_idSWS_FT_FI26
Number of Residues2
DetailsLIPID: S-palmitoyl cysteine => ECO:0000269|PubMed:21076176
ChainResidueDetails
AALA110
EALA110

Catalytic Information from CSA
site_idMCSA1
Number of Residues8
DetailsM-CSA 510
ChainResidueDetails
KASP70metal ligand
KGLU96metal ligand
KTYR171electrostatic stabiliser, metal ligand
KASP210increase nucleophilicity, metal ligand, proton acceptor
KASN212
KASP283electrostatic stabiliser
KASP308metal ligand
KHIS309electrostatic stabiliser, metal ligand

222415

PDB entries from 2024-07-10

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