5DFI

Human APE1 phosphorothioate substrate complex

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
B	0003677	molecular_function	DNA binding
B	0003824	molecular_function	catalytic activity
B	0004518	molecular_function	nuclease activity
B	0004519	molecular_function	endonuclease activity
B	0006281	biological_process	DNA repair

Functional Information from PDB Data

site_id	AC1
Number of Residues	7
Details	binding site for residue EDO A 401

Chain	Residue
A	LEU44
A	TYR45
A	ASN277
A	HOH548
A	HOH553
A	HOH622
A	HOH624

---

site_id	AC2
Number of Residues	6
Details	binding site for residue EDO A 402

Chain	Residue
A	GLY239
A	PHE240
A	HOH507
A	HOH546
A	ASP189
A	PHE192

---

site_id	AC3
Number of Residues	6
Details	binding site for residue EDO A 403

Chain	Residue
A	PHE266
A	THR268
A	TYR269
A	ASP308
P	DC12
V	DG12

---

site_id	AC4
Number of Residues	6
Details	binding site for residue CL A 404

Chain	Residue
A	GLU101
A	TYR118
A	TRP119
A	HOH545
B	HIS116
B	ARG136

---

site_id	AC5
Number of Residues	5
Details	binding site for residue EDO B 401

Chain	Residue
B	TYR45
B	ARG274
B	ASN277
B	HOH507
B	HOH586

---

site_id	AC6
Number of Residues	6
Details	binding site for residue EDO B 402

Chain	Residue
B	ASP189
B	PHE192
B	GLY239
B	PHE240
B	HOH571
B	HOH623

---

site_id	AC7
Number of Residues	3
Details	binding site for residue CL B 403

Chain	Residue
B	GLY145
B	ARG156
B	VAL157

---

site_id	AC8
Number of Residues	5
Details	binding site for residue EDO V 101

Chain	Residue
B	ARG177
B	MET270
B	MET271
V	DG1
V	DG2

---

site_id	AC9
Number of Residues	20
Details	binding site for residues OMC P 10 and 48Z P 11

Chain	Residue
A	GLU96
A	TYR171
A	ASN174
A	ARG177
A	ARG181
A	ASN212
A	ALA230
A	PHE266
A	TRP280
A	HIS309
P	DG9
P	DC12
P	HOH101
P	HOH109
P	HOH111
P	HOH112
P	HOH113
P	HOH116
P	HOH120
V	DG12

---

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	2
Details	ACT_SITE: ACT_SITE => ECO:0000269|PubMed:15380100

Chain	Residue	Details
A	TYR171
B	TYR171

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	ACT_SITE: Proton donor/acceptor => ECO:0000269|PubMed:9351835, ECO:0007744|PDB:1BIX

Chain	Residue	Details
A	ASP210
B	ASP210

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	ACT_SITE: Proton acceptor => ECO:0000255|PROSITE-ProRule:PRU00764

Chain	Residue	Details
A	HIS309
B	HIS309

---

site_id	SWS_FT_FI4
Number of Residues	12
Details	BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00764

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

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	SITE: Transition state stabilizer => ECO:0000269|PubMed:8932375

Chain	Residue	Details
A	ASN212
B	ASN212

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	SITE: Important for catalytic activity => ECO:0000269|PubMed:21762700, ECO:0000269|PubMed:9804799

Chain	Residue	Details
A	ASP283
B	ASP283

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	SITE: Interaction with DNA substrate

Chain	Residue	Details
A	HIS309
B	HIS309

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
A	SER54
B	SER54

---

site_id	SWS_FT_FI9
Number of Residues	4
Details	MOD_RES: S-nitrosocysteine; alternate => ECO:0000269|PubMed:17403694

Chain	Residue	Details
A	CYS65
A	CYS93
B	CYS65
B	CYS93

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861

Chain	Residue	Details
A	LYS197
B	LYS197

---

site_id	SWS_FT_FI11
Number of Residues	2
Details	MOD_RES: Phosphothreonine; by CDK5 => ECO:0000250|UniProtKB:P28352

Chain	Residue	Details
A	THR233
B	THR233

---

site_id	SWS_FT_FI12
Number of Residues	2
Details	MOD_RES: S-nitrosocysteine => ECO:0000269|PubMed:17403694

Chain	Residue	Details
A	CYS310
B	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

---

site_id	MCSA2
Number of Residues	8
Details	M-CSA 510

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

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