4QHD

Crystal structure of apo human APE1

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003677	molecular_function	DNA binding
A	0003824	molecular_function	catalytic activity
A	0004518	molecular_function	nuclease activity
A	0004519	molecular_function	endonuclease activity
A	0006281	biological_process	DNA repair

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 401

Chain	Residue
A	ASN174
A	ALA230
A	PHE266
A	TRP280
A	HOH610
A	HOH672

---

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 402

Chain	Residue
A	TYR118
A	HOH647
A	SER115
A	HIS116
A	GLN117

---

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 403

Chain	Residue
A	PRO248
A	SER288
A	HIS289
A	SER290
A	HOH556

---

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 404

Chain	Residue
A	HIS215
A	GLU216
A	ARG237
A	GLN238
A	GLY241

---

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	1
Details	ACT_SITE: ACT_SITE => ECO:0000269|PubMed:15380100

Chain	Residue	Details
A	TYR171

---

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

Chain	Residue	Details
A	ASP210

---

site_id	SWS_FT_FI3
Number of Residues	1
Details	ACT_SITE: Proton acceptor => ECO:0000255|PROSITE-ProRule:PRU00764

Chain	Residue	Details
A	HIS309

---

site_id	SWS_FT_FI4
Number of Residues	6
Details	BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00764

Chain	Residue	Details
A	ASN68
A	GLU96
A	ASP210
A	ASN212
A	ASP308
A	HIS309

---

site_id	SWS_FT_FI5
Number of Residues	1
Details	SITE: Transition state stabilizer => ECO:0000269|PubMed:8932375

Chain	Residue	Details
A	ASN212

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	SITE: Important for catalytic activity => ECO:0000269|PubMed:21762700, ECO:0000269|PubMed:9804799

Chain	Residue	Details
A	ASP283

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	SITE: Interaction with DNA substrate

Chain	Residue	Details
A	HIS309

---

site_id	SWS_FT_FI8
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
A	SER54

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	MOD_RES: S-nitrosocysteine; alternate => ECO:0000269|PubMed:17403694

Chain	Residue	Details
A	CYS65
A	CYS93

---

site_id	SWS_FT_FI10
Number of Residues	1
Details	MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861

Chain	Residue	Details
A	LYS197

---

site_id	SWS_FT_FI11
Number of Residues	1
Details	MOD_RES: Phosphothreonine; by CDK5 => ECO:0000250|UniProtKB:P28352

Chain	Residue	Details
A	THR233

---

site_id	SWS_FT_FI12
Number of Residues	1
Details	MOD_RES: S-nitrosocysteine => ECO:0000269|PubMed:17403694

Chain	Residue	Details
A	CYS310

---

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	8
Details	M-CSA 510

Chain	Residue	Details
A	ASP70	metal ligand
A	GLU96	metal ligand
A	TYR171	electrostatic stabiliser, metal ligand
A	ASP210	increase nucleophilicity, metal ligand, proton acceptor
A	ASN212
A	ASP283	electrostatic stabiliser
A	ASP308	metal ligand
A	HIS309	electrostatic stabiliser, metal ligand

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