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Human APE1 substrate complex with an C/C mismatch adjacent the THF

Functional Information from GO Data
ChainGOidnamespacecontents
A0000723biological_processtelomere maintenance
A0000781cellular_componentchromosome, telomeric region
A0003677molecular_functionDNA binding
A0003684molecular_functiondamaged DNA binding
A0003691molecular_functiondouble-stranded telomeric DNA binding
A0003713molecular_functiontranscription coactivator activity
A0003714molecular_functiontranscription corepressor activity
A0003723molecular_functionRNA binding
A0003824molecular_functioncatalytic activity
A0003906molecular_functionDNA-(apurinic or apyrimidinic site) endonuclease activity
A0004518molecular_functionnuclease activity
A0004519molecular_functionendonuclease activity
A0004520molecular_functionDNA endonuclease activity
A0004523molecular_functionRNA-DNA hybrid ribonuclease activity
A0004527molecular_functionexonuclease activity
A0004528molecular_functionphosphodiesterase I activity
A0004844molecular_functionuracil DNA N-glycosylase activity
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005730cellular_componentnucleolus
A0005737cellular_componentcytoplasm
A0005739cellular_componentmitochondrion
A0005783cellular_componentendoplasmic reticulum
A0005813cellular_componentcentrosome
A0005840cellular_componentribosome
A0006281biological_processDNA repair
A0006284biological_processbase-excision repair
A0006287biological_processbase-excision repair, gap-filling
A0006308biological_processDNA catabolic process
A0006310biological_processDNA recombination
A0008081molecular_functionphosphoric diester hydrolase activity
A0008296molecular_function3'-5'-DNA exonuclease activity
A0008309molecular_functiondouble-stranded DNA exodeoxyribonuclease activity
A0008311molecular_functiondouble-stranded DNA 3'-5' DNA exonuclease activity
A0008408molecular_function3'-5' exonuclease activity
A0016491molecular_functionoxidoreductase activity
A0016607cellular_componentnuclear speck
A0016890molecular_functionsite-specific endodeoxyribonuclease activity, specific for altered base
A0031490molecular_functionchromatin DNA binding
A0042981biological_processregulation of apoptotic process
A0043488biological_processregulation of mRNA stability
A0044029biological_processpositive regulation of gene expression via chromosomal CpG island demethylation
A0045454biological_processcell redox homeostasis
A0045892biological_processnegative regulation of DNA-templated transcription
A0045944biological_processpositive regulation of transcription by RNA polymerase II
A0046872molecular_functionmetal ion binding
A0048471cellular_componentperinuclear region of cytoplasm
A0052720molecular_functionclass II DNA-(apurinic or apyrimidinic site) endonuclease activity
A0090580molecular_functionphosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands
A0097698biological_processtelomere maintenance via base-excision repair
A0140431molecular_functionDNA-(abasic site) binding
B0000723biological_processtelomere maintenance
B0000781cellular_componentchromosome, telomeric region
B0003677molecular_functionDNA binding
B0003684molecular_functiondamaged DNA binding
B0003691molecular_functiondouble-stranded telomeric DNA binding
B0003713molecular_functiontranscription coactivator activity
B0003714molecular_functiontranscription corepressor activity
B0003723molecular_functionRNA binding
B0003824molecular_functioncatalytic activity
B0003906molecular_functionDNA-(apurinic or apyrimidinic site) endonuclease activity
B0004518molecular_functionnuclease activity
B0004519molecular_functionendonuclease activity
B0004520molecular_functionDNA endonuclease activity
B0004523molecular_functionRNA-DNA hybrid ribonuclease activity
B0004527molecular_functionexonuclease activity
B0004528molecular_functionphosphodiesterase I activity
B0004844molecular_functionuracil DNA N-glycosylase activity
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005654cellular_componentnucleoplasm
B0005730cellular_componentnucleolus
B0005737cellular_componentcytoplasm
B0005739cellular_componentmitochondrion
B0005783cellular_componentendoplasmic reticulum
B0005813cellular_componentcentrosome
B0005840cellular_componentribosome
B0006281biological_processDNA repair
B0006284biological_processbase-excision repair
B0006287biological_processbase-excision repair, gap-filling
B0006308biological_processDNA catabolic process
B0006310biological_processDNA recombination
B0008081molecular_functionphosphoric diester hydrolase activity
B0008296molecular_function3'-5'-DNA exonuclease activity
B0008309molecular_functiondouble-stranded DNA exodeoxyribonuclease activity
B0008311molecular_functiondouble-stranded DNA 3'-5' DNA exonuclease activity
B0008408molecular_function3'-5' exonuclease activity
B0016491molecular_functionoxidoreductase activity
B0016607cellular_componentnuclear speck
B0016890molecular_functionsite-specific endodeoxyribonuclease activity, specific for altered base
B0031490molecular_functionchromatin DNA binding
B0042981biological_processregulation of apoptotic process
B0043488biological_processregulation of mRNA stability
B0044029biological_processpositive regulation of gene expression via chromosomal CpG island demethylation
B0045454biological_processcell redox homeostasis
B0045892biological_processnegative regulation of DNA-templated transcription
B0045944biological_processpositive regulation of transcription by RNA polymerase II
B0046872molecular_functionmetal ion binding
B0048471cellular_componentperinuclear region of cytoplasm
B0052720molecular_functionclass II DNA-(apurinic or apyrimidinic site) endonuclease activity
B0090580molecular_functionphosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands
B0097698biological_processtelomere maintenance via base-excision repair
B0140431molecular_functionDNA-(abasic site) binding
Functional Information from PDB Data
site_idAC1
Number of Residues6
Detailsbinding site for residue EDO A 401
ChainResidue
ALEU44
ATYR45
AASN277
AHOH522
AHOH528
AHOH537

Functional Information from PROSITE/UniProt
site_idPS00726
Number of Residues10
DetailsAP_NUCLEASE_F1_1 AP endonucleases family 1 signature 1. PDILCLQETK
ChainResidueDetails
APRO89-LYS98

site_idPS00727
Number of Residues17
DetailsAP_NUCLEASE_F1_2 AP endonucleases family 1 signature 2. DSFRHlypntpyaYTFW
ChainResidueDetails
AASP251-TRP267

site_idPS00728
Number of Residues12
DetailsAP_NUCLEASE_F1_3 AP endonucleases family 1 signature 3. NvGwRLDYfLlS
ChainResidueDetails
AASN277-SER288

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsACT_SITE: ACT_SITE => ECO:0000269|PubMed:15380100
ChainResidueDetails
ATYR171
BTYR171

site_idSWS_FT_FI2
Number of Residues2
DetailsACT_SITE: Proton donor/acceptor => ECO:0000269|PubMed:9351835, ECO:0007744|PDB:1BIX
ChainResidueDetails
AASP210
BASP210

site_idSWS_FT_FI3
Number of Residues2
DetailsACT_SITE: Proton acceptor => ECO:0000255|PROSITE-ProRule:PRU00764
ChainResidueDetails
AHIS309
BHIS309

site_idSWS_FT_FI4
Number of Residues12
DetailsBINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00764
ChainResidueDetails
AASN68
BASN212
BASP308
BHIS309
AGLU96
AASP210
AASN212
AASP308
AHIS309
BASN68
BGLU96
BASP210

site_idSWS_FT_FI5
Number of Residues2
DetailsSITE: Cleavage; by granzyme A
ChainResidueDetails
ALYS31
BLYS31

site_idSWS_FT_FI6
Number of Residues2
DetailsSITE: Transition state stabilizer => ECO:0000269|PubMed:8932375
ChainResidueDetails
AASN212
BASN212

site_idSWS_FT_FI7
Number of Residues2
DetailsSITE: Important for catalytic activity => ECO:0000269|PubMed:21762700, ECO:0000269|PubMed:9804799
ChainResidueDetails
AASP283
BASP283

site_idSWS_FT_FI8
Number of Residues2
DetailsSITE: Interaction with DNA substrate
ChainResidueDetails
AHIS309
BHIS309

site_idSWS_FT_FI9
Number of Residues4
DetailsMOD_RES: N6-acetyllysine; by EP300 => ECO:0000269|PubMed:14633989
ChainResidueDetails
ALYS6
ALYS7
BLYS6
BLYS7

site_idSWS_FT_FI10
Number of Residues8
DetailsMOD_RES: N6-acetyllysine => ECO:0000269|PubMed:20699270
ChainResidueDetails
ALYS27
ALYS31
ALYS32
ALYS35
BLYS27
BLYS31
BLYS32
BLYS35

site_idSWS_FT_FI11
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163
ChainResidueDetails
ASER54
BSER54

site_idSWS_FT_FI12
Number of Residues4
DetailsMOD_RES: S-nitrosocysteine; alternate => ECO:0000269|PubMed:17403694
ChainResidueDetails
ACYS65
ACYS93
BCYS65
BCYS93

site_idSWS_FT_FI13
Number of Residues2
DetailsMOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861
ChainResidueDetails
ALYS197
BLYS197

site_idSWS_FT_FI14
Number of Residues2
DetailsMOD_RES: Phosphothreonine; by CDK5 => ECO:0000250|UniProtKB:P28352
ChainResidueDetails
ATHR233
BTHR233

site_idSWS_FT_FI15
Number of Residues2
DetailsMOD_RES: S-nitrosocysteine => ECO:0000269|PubMed:17403694
ChainResidueDetails
ACYS310
BCYS310

Catalytic Information from CSA
site_idMCSA1
Number of Residues8
DetailsM-CSA 510
ChainResidueDetails
AASP70metal ligand
AGLU96metal ligand
ATYR171electrostatic stabiliser, metal ligand
AASP210increase nucleophilicity, metal ligand, proton acceptor
AASN212
AASP283electrostatic stabiliser
AASP308metal ligand
AHIS309electrostatic stabiliser, metal ligand

site_idMCSA2
Number of Residues8
DetailsM-CSA 510
ChainResidueDetails
BASP70metal ligand
BGLU96metal ligand
BTYR171electrostatic stabiliser, metal ligand
BASP210increase nucleophilicity, metal ligand, proton acceptor
BASN212
BASP283electrostatic stabiliser
BASP308metal ligand
BHIS309electrostatic stabiliser, metal ligand

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PDB entries from 2024-11-06

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