Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2ISI

Crystal structure of Ape1 from Homo sapiens in a new crystal form complexed with a ligand

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000723	biological_process	telomere maintenance
A	0000781	cellular_component	chromosome, telomeric region
A	0003677	molecular_function	DNA binding
A	0003684	molecular_function	damaged DNA binding
A	0003691	molecular_function	double-stranded telomeric DNA binding
A	0003713	molecular_function	transcription coactivator activity
A	0003714	molecular_function	transcription corepressor activity
A	0003723	molecular_function	RNA binding
A	0003824	molecular_function	catalytic activity
A	0003906	molecular_function	DNA-(apurinic or apyrimidinic site) endonuclease activity
A	0004518	molecular_function	nuclease activity
A	0004519	molecular_function	endonuclease activity
A	0004520	molecular_function	DNA endonuclease activity
A	0004523	molecular_function	RNA-DNA hybrid ribonuclease activity
A	0004527	molecular_function	exonuclease activity
A	0004528	molecular_function	phosphodiesterase I activity
A	0004844	molecular_function	uracil DNA N-glycosylase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005730	cellular_component	nucleolus
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0005783	cellular_component	endoplasmic reticulum
A	0005813	cellular_component	centrosome
A	0005840	cellular_component	ribosome
A	0006281	biological_process	DNA repair
A	0006284	biological_process	base-excision repair
A	0006287	biological_process	base-excision repair, gap-filling
A	0006308	biological_process	DNA catabolic process
A	0006310	biological_process	DNA recombination
A	0008081	molecular_function	phosphoric diester hydrolase activity
A	0008296	molecular_function	3'-5'-DNA exonuclease activity
A	0008309	molecular_function	double-stranded DNA exodeoxyribonuclease activity
A	0008311	molecular_function	double-stranded DNA 3'-5' DNA exonuclease activity
A	0008408	molecular_function	3'-5' exonuclease activity
A	0016491	molecular_function	oxidoreductase activity
A	0016607	cellular_component	nuclear speck
A	0016890	molecular_function	site-specific endodeoxyribonuclease activity, specific for altered base
A	0031490	molecular_function	chromatin DNA binding
A	0042981	biological_process	regulation of apoptotic process
A	0043488	biological_process	regulation of mRNA stability
A	0044029	biological_process	positive regulation of gene expression via chromosomal CpG island demethylation
A	0045454	biological_process	cell redox homeostasis
A	0045892	biological_process	negative regulation of DNA-templated transcription
A	0045944	biological_process	positive regulation of transcription by RNA polymerase II
A	0046872	molecular_function	metal ion binding
A	0048471	cellular_component	perinuclear region of cytoplasm
A	0052720	molecular_function	class II DNA-(apurinic or apyrimidinic site) endonuclease activity
A	0090580	molecular_function	phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands
A	0097698	biological_process	telomere maintenance via base-excision repair
A	0140431	molecular_function	DNA-(abasic site) binding
B	0000723	biological_process	telomere maintenance
B	0000781	cellular_component	chromosome, telomeric region
B	0003677	molecular_function	DNA binding
B	0003684	molecular_function	damaged DNA binding
B	0003691	molecular_function	double-stranded telomeric DNA binding
B	0003713	molecular_function	transcription coactivator activity
B	0003714	molecular_function	transcription corepressor activity
B	0003723	molecular_function	RNA binding
B	0003824	molecular_function	catalytic activity
B	0003906	molecular_function	DNA-(apurinic or apyrimidinic site) endonuclease activity
B	0004518	molecular_function	nuclease activity
B	0004519	molecular_function	endonuclease activity
B	0004520	molecular_function	DNA endonuclease activity
B	0004523	molecular_function	RNA-DNA hybrid ribonuclease activity
B	0004527	molecular_function	exonuclease activity
B	0004528	molecular_function	phosphodiesterase I activity
B	0004844	molecular_function	uracil DNA N-glycosylase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005730	cellular_component	nucleolus
B	0005737	cellular_component	cytoplasm
B	0005739	cellular_component	mitochondrion
B	0005783	cellular_component	endoplasmic reticulum
B	0005813	cellular_component	centrosome
B	0005840	cellular_component	ribosome
B	0006281	biological_process	DNA repair
B	0006284	biological_process	base-excision repair
B	0006287	biological_process	base-excision repair, gap-filling
B	0006308	biological_process	DNA catabolic process
B	0006310	biological_process	DNA recombination
B	0008081	molecular_function	phosphoric diester hydrolase activity
B	0008296	molecular_function	3'-5'-DNA exonuclease activity
B	0008309	molecular_function	double-stranded DNA exodeoxyribonuclease activity
B	0008311	molecular_function	double-stranded DNA 3'-5' DNA exonuclease activity
B	0008408	molecular_function	3'-5' exonuclease activity
B	0016491	molecular_function	oxidoreductase activity
B	0016607	cellular_component	nuclear speck
B	0016890	molecular_function	site-specific endodeoxyribonuclease activity, specific for altered base
B	0031490	molecular_function	chromatin DNA binding
B	0042981	biological_process	regulation of apoptotic process
B	0043488	biological_process	regulation of mRNA stability
B	0044029	biological_process	positive regulation of gene expression via chromosomal CpG island demethylation
B	0045454	biological_process	cell redox homeostasis
B	0045892	biological_process	negative regulation of DNA-templated transcription
B	0045944	biological_process	positive regulation of transcription by RNA polymerase II
B	0046872	molecular_function	metal ion binding
B	0048471	cellular_component	perinuclear region of cytoplasm
B	0052720	molecular_function	class II DNA-(apurinic or apyrimidinic site) endonuclease activity
B	0090580	molecular_function	phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands
B	0097698	biological_process	telomere maintenance via base-excision repair
B	0140431	molecular_function	DNA-(abasic site) binding
C	0000723	biological_process	telomere maintenance
C	0000781	cellular_component	chromosome, telomeric region
C	0003677	molecular_function	DNA binding
C	0003684	molecular_function	damaged DNA binding
C	0003691	molecular_function	double-stranded telomeric DNA binding
C	0003713	molecular_function	transcription coactivator activity
C	0003714	molecular_function	transcription corepressor activity
C	0003723	molecular_function	RNA binding
C	0003824	molecular_function	catalytic activity
C	0003906	molecular_function	DNA-(apurinic or apyrimidinic site) endonuclease activity
C	0004518	molecular_function	nuclease activity
C	0004519	molecular_function	endonuclease activity
C	0004520	molecular_function	DNA endonuclease activity
C	0004523	molecular_function	RNA-DNA hybrid ribonuclease activity
C	0004527	molecular_function	exonuclease activity
C	0004528	molecular_function	phosphodiesterase I activity
C	0004844	molecular_function	uracil DNA N-glycosylase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005730	cellular_component	nucleolus
C	0005737	cellular_component	cytoplasm
C	0005739	cellular_component	mitochondrion
C	0005783	cellular_component	endoplasmic reticulum
C	0005813	cellular_component	centrosome
C	0005840	cellular_component	ribosome
C	0006281	biological_process	DNA repair
C	0006284	biological_process	base-excision repair
C	0006287	biological_process	base-excision repair, gap-filling
C	0006308	biological_process	DNA catabolic process
C	0006310	biological_process	DNA recombination
C	0008081	molecular_function	phosphoric diester hydrolase activity
C	0008296	molecular_function	3'-5'-DNA exonuclease activity
C	0008309	molecular_function	double-stranded DNA exodeoxyribonuclease activity
C	0008311	molecular_function	double-stranded DNA 3'-5' DNA exonuclease activity
C	0008408	molecular_function	3'-5' exonuclease activity
C	0016491	molecular_function	oxidoreductase activity
C	0016607	cellular_component	nuclear speck
C	0016890	molecular_function	site-specific endodeoxyribonuclease activity, specific for altered base
C	0031490	molecular_function	chromatin DNA binding
C	0042981	biological_process	regulation of apoptotic process
C	0043488	biological_process	regulation of mRNA stability
C	0044029	biological_process	positive regulation of gene expression via chromosomal CpG island demethylation
C	0045454	biological_process	cell redox homeostasis
C	0045892	biological_process	negative regulation of DNA-templated transcription
C	0045944	biological_process	positive regulation of transcription by RNA polymerase II
C	0046872	molecular_function	metal ion binding
C	0048471	cellular_component	perinuclear region of cytoplasm
C	0052720	molecular_function	class II DNA-(apurinic or apyrimidinic site) endonuclease activity
C	0090580	molecular_function	phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands
C	0097698	biological_process	telomere maintenance via base-excision repair
C	0140431	molecular_function	DNA-(abasic site) binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PO4 A 400

Chain	Residue
A	ASN174
A	ALA230
A	TRP280
A	HOH411

site_id	AC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PO4 B 401

Chain	Residue
B	ASN174
B	ASN212
B	ALA230

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG A 402

Chain	Residue
A	HOH414
A	ASP70
A	GLU96

site_id	AC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MG B 403

Chain	Residue
B	ASP70
B	GLU96

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG C 404

Chain	Residue
C	ASN68
C	ASP70
C	GLU96
C	ASP308

Functional Information from PROSITE/UniProt

site_id	PS00726
Number of Residues	10
Details	AP_NUCLEASE_F1_1 AP endonucleases family 1 signature 1. PDILCLQETK

Chain	Residue	Details
A	PRO89-LYS98

site_id	PS00727
Number of Residues	17
Details	AP_NUCLEASE_F1_2 AP endonucleases family 1 signature 2. DSFRHlypntpyaYTFW

Chain	Residue	Details
A	ASP251-TRP267

site_id	PS00728
Number of Residues	12
Details	AP_NUCLEASE_F1_3 AP endonucleases family 1 signature 3. NvGwRLDYfLlS

Chain	Residue	Details
A	ASN277-SER288

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3
Details	ACT_SITE: ACT_SITE => ECO:0000269\|PubMed:15380100

Chain	Residue	Details
A	VAL172
B	VAL172
C	VAL172

site_id	SWS_FT_FI2
Number of Residues	3
Details	ACT_SITE: Proton donor/acceptor => ECO:0000269\|PubMed:9351835, ECO:0007744\|PDB:1BIX

Chain	Residue	Details
A	LEU211
B	LEU211
C	LEU211

site_id	SWS_FT_FI3
Number of Residues	3
Details	ACT_SITE: Proton acceptor => ECO:0000255\|PROSITE-ProRule:PRU00764

Chain	Residue	Details
A	CYS310
B	CYS310
C	CYS310

site_id	SWS_FT_FI4
Number of Residues	18
Details	BINDING: BINDING => ECO:0000255\|PROSITE-ProRule:PRU00764

Chain	Residue	Details
A	VAL69
B	VAL213
B	HIS309
B	CYS310
C	VAL69
C	THR97
C	LEU211
C	VAL213
C	HIS309
C	CYS310
A	THR97
A	LEU211
A	VAL213
A	HIS309
A	CYS310
B	VAL69
B	THR97
B	LEU211

site_id	SWS_FT_FI5
Number of Residues	3
Details	SITE: Cleavage; by granzyme A

Chain	Residue	Details
A	LYS32
B	LYS32
C	LYS32

site_id	SWS_FT_FI6
Number of Residues	3
Details	SITE: Transition state stabilizer => ECO:0000269\|PubMed:8932375

Chain	Residue	Details
A	VAL213
B	VAL213
C	VAL213

site_id	SWS_FT_FI7
Number of Residues	3
Details	SITE: Important for catalytic activity => ECO:0000269\|PubMed:21762700, ECO:0000269\|PubMed:9804799

Chain	Residue	Details
A	TYR284
B	TYR284
C	TYR284

site_id	SWS_FT_FI8
Number of Residues	3
Details	SITE: Interaction with DNA substrate

Chain	Residue	Details
A	CYS310
B	CYS310
C	CYS310

site_id	SWS_FT_FI9
Number of Residues	6
Details	MOD_RES: N6-acetyllysine; by EP300 => ECO:0000269\|PubMed:14633989

Chain	Residue	Details
A	LYS7
A	GLY8
B	LYS7
B	GLY8
C	LYS7
C	GLY8

site_id	SWS_FT_FI10
Number of Residues	12
Details	MOD_RES: N6-acetyllysine => ECO:0000269\|PubMed:20699270

Chain	Residue	Details
A	THR28
C	LYS32
C	ASN33
C	GLU36
A	LYS32
A	ASN33
A	GLU36
B	THR28
B	LYS32
B	ASN33
B	GLU36
C	THR28

site_id	SWS_FT_FI11
Number of Residues	3
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	PRO55
B	PRO55
C	PRO55

site_id	SWS_FT_FI12
Number of Residues	6
Details	MOD_RES: S-nitrosocysteine; alternate => ECO:0000269\|PubMed:17403694

Chain	Residue	Details
A	SER66
A	LEU94
B	SER66
B	LEU94
C	SER66
C	LEU94

site_id	SWS_FT_FI13
Number of Residues	3
Details	MOD_RES: N6-acetyllysine => ECO:0007744\|PubMed:19608861

Chain	Residue	Details
A	GLY198
B	GLY198
C	GLY198

site_id	SWS_FT_FI14
Number of Residues	3
Details	MOD_RES: Phosphothreonine; by CDK5 => ECO:0000250\|UniProtKB:P28352

Chain	Residue	Details
A	PRO234
B	PRO234
C	PRO234

site_id	SWS_FT_FI15
Number of Residues	3
Details	MOD_RES: S-nitrosocysteine => ECO:0000269\|PubMed:17403694

Chain	Residue	Details
A	PRO311
B	PRO311
C	PRO311

Catalytic Information from CSA

site_id	CSA1
Number of Residues	5
Details	Annotated By Reference To The Literature 1ako

Chain	Residue	Details
A	ASN212
A	HIS309
A	ASN68
A	ASP283
A	ASP210

site_id	CSA2
Number of Residues	5
Details	Annotated By Reference To The Literature 1ako

Chain	Residue	Details
B	ASN212
B	HIS309
B	ASN68
B	ASP283
B	ASP210

site_id	CSA3
Number of Residues	5
Details	Annotated By Reference To The Literature 1ako

Chain	Residue	Details
C	ASN212
C	HIS309
C	ASN68
C	ASP283
C	ASP210

site_id	MCSA1
Number of Residues	8
Details	M-CSA 510

Chain	Residue	Details
A	GLY71	metal ligand
A	THR97	metal ligand
A	VAL172	electrostatic stabiliser, metal ligand
A	LEU211	increase nucleophilicity, metal ligand, proton acceptor
A	VAL213
A	TYR284	electrostatic stabiliser
A	HIS309	metal ligand
A	CYS310	electrostatic stabiliser, metal ligand

site_id	MCSA2
Number of Residues	8
Details	M-CSA 510

Chain	Residue	Details
B	GLY71	metal ligand
B	THR97	metal ligand
B	VAL172	electrostatic stabiliser, metal ligand
B	LEU211	increase nucleophilicity, metal ligand, proton acceptor
B	VAL213
B	TYR284	electrostatic stabiliser
B	HIS309	metal ligand
B	CYS310	electrostatic stabiliser, metal ligand

site_id	MCSA3
Number of Residues	8
Details	M-CSA 510

Chain	Residue	Details
C	GLY71	metal ligand
C	THR97	metal ligand
C	VAL172	electrostatic stabiliser, metal ligand
C	LEU211	increase nucleophilicity, metal ligand, proton acceptor
C	VAL213
C	TYR284	electrostatic stabiliser
C	HIS309	metal ligand
C	CYS310	electrostatic stabiliser, metal ligand

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)