6S1O

Human polymerase delta holoenzyme Conformer 3

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000109	cellular_component	nucleotide-excision repair complex
A	0000166	molecular_function	nucleotide binding
A	0000731	biological_process	DNA synthesis involved in DNA repair
A	0000781	cellular_component	chromosome, telomeric region
A	0003676	molecular_function	nucleic acid binding
A	0003677	molecular_function	DNA binding
A	0003682	molecular_function	chromatin binding
A	0003684	molecular_function	damaged DNA binding
A	0003887	molecular_function	DNA-directed DNA polymerase activity
A	0004518	molecular_function	nuclease activity
A	0004527	molecular_function	exonuclease activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005829	cellular_component	cytosol
A	0006260	biological_process	DNA replication
A	0006261	biological_process	DNA-templated DNA replication
A	0006281	biological_process	DNA repair
A	0006287	biological_process	base-excision repair, gap-filling
A	0006297	biological_process	nucleotide-excision repair, DNA gap filling
A	0006974	biological_process	DNA damage response
A	0008270	molecular_function	zinc ion binding
A	0008296	molecular_function	3'-5'-DNA exonuclease activity
A	0008408	molecular_function	3'-5' exonuclease activity
A	0009411	biological_process	response to UV
A	0016020	cellular_component	membrane
A	0016235	cellular_component	aggresome
A	0016740	molecular_function	transferase activity
A	0016779	molecular_function	nucleotidyltransferase activity
A	0016787	molecular_function	hydrolase activity
A	0019899	molecular_function	enzyme binding
A	0034061	molecular_function	DNA polymerase activity
A	0034644	biological_process	cellular response to UV
A	0043625	cellular_component	delta DNA polymerase complex
A	0045004	biological_process	DNA replication proofreading
A	0046872	molecular_function	metal ion binding
A	0051536	molecular_function	iron-sulfur cluster binding
A	0051539	molecular_function	4 iron, 4 sulfur cluster binding
A	0055089	biological_process	fatty acid homeostasis
A	0070987	biological_process	error-free translesion synthesis
A	0071897	biological_process	DNA biosynthetic process
B	0003677	molecular_function	DNA binding
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0006260	biological_process	DNA replication
B	0006261	biological_process	DNA-templated DNA replication
B	0006271	biological_process	DNA strand elongation involved in DNA replication
B	0006281	biological_process	DNA repair
B	0006974	biological_process	DNA damage response
B	0016035	cellular_component	zeta DNA polymerase complex
B	0042276	biological_process	error-prone translesion synthesis
B	0043625	cellular_component	delta DNA polymerase complex
B	0071897	biological_process	DNA biosynthetic process
C	0000731	biological_process	DNA synthesis involved in DNA repair
C	0003887	molecular_function	DNA-directed DNA polymerase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0006260	biological_process	DNA replication
C	0006261	biological_process	DNA-templated DNA replication
C	0006271	biological_process	DNA strand elongation involved in DNA replication
C	0006281	biological_process	DNA repair
C	0006297	biological_process	nucleotide-excision repair, DNA gap filling
C	0006298	biological_process	mismatch repair
C	0006974	biological_process	DNA damage response
C	0016035	cellular_component	zeta DNA polymerase complex
C	0030674	molecular_function	protein-macromolecule adaptor activity
C	0042276	biological_process	error-prone translesion synthesis
C	0043625	cellular_component	delta DNA polymerase complex
C	0071897	biological_process	DNA biosynthetic process
C	1904161	biological_process	DNA synthesis involved in UV-damage excision repair
D	0000731	biological_process	DNA synthesis involved in DNA repair
D	0001938	biological_process	positive regulation of endothelial cell proliferation
D	0003887	molecular_function	DNA-directed DNA polymerase activity
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0006260	biological_process	DNA replication
D	0006261	biological_process	DNA-templated DNA replication
D	0006281	biological_process	DNA repair
D	0006974	biological_process	DNA damage response
D	0043625	cellular_component	delta DNA polymerase complex
E	0000122	biological_process	negative regulation of transcription by RNA polymerase II
E	0000307	cellular_component	cyclin-dependent protein kinase holoenzyme complex
E	0000701	molecular_function	purine-specific mismatch base pair DNA N-glycosylase activity
E	0000781	cellular_component	chromosome, telomeric region
E	0000785	cellular_component	chromatin
E	0001673	cellular_component	male germ cell nucleus
E	0003677	molecular_function	DNA binding
E	0003682	molecular_function	chromatin binding
E	0003684	molecular_function	damaged DNA binding
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005652	cellular_component	nuclear lamina
E	0005654	cellular_component	nucleoplasm
E	0005657	cellular_component	replication fork
E	0005813	cellular_component	centrosome
E	0006260	biological_process	DNA replication
E	0006272	biological_process	leading strand elongation
E	0006275	biological_process	regulation of DNA replication
E	0006281	biological_process	DNA repair
E	0006287	biological_process	base-excision repair, gap-filling
E	0006298	biological_process	mismatch repair
E	0006325	biological_process	chromatin organization
E	0006974	biological_process	DNA damage response
E	0006979	biological_process	response to oxidative stress
E	0007507	biological_process	heart development
E	0016604	cellular_component	nuclear body
E	0019899	molecular_function	enzyme binding
E	0019985	biological_process	translesion synthesis
E	0030331	molecular_function	nuclear estrogen receptor binding
E	0030337	molecular_function	DNA polymerase processivity factor activity
E	0030855	biological_process	epithelial cell differentiation
E	0030894	cellular_component	replisome
E	0030971	molecular_function	receptor tyrosine kinase binding
E	0031297	biological_process	replication fork processing
E	0032139	molecular_function	dinucleotide insertion or deletion binding
E	0032355	biological_process	response to estradiol
E	0032405	molecular_function	MutLalpha complex binding
E	0033993	biological_process	response to lipid
E	0034644	biological_process	cellular response to UV
E	0035035	molecular_function	histone acetyltransferase binding
E	0042802	molecular_function	identical protein binding
E	0043596	cellular_component	nuclear replication fork
E	0043626	cellular_component	PCNA complex
E	0044849	biological_process	estrous cycle
E	0044877	molecular_function	protein-containing complex binding
E	0045739	biological_process	positive regulation of DNA repair
E	0045740	biological_process	positive regulation of DNA replication
E	0046686	biological_process	response to cadmium ion
E	0070062	cellular_component	extracellular exosome
E	0070182	molecular_function	DNA polymerase binding
E	0070301	biological_process	cellular response to hydrogen peroxide
E	0070557	cellular_component	PCNA-p21 complex
E	0071466	biological_process	cellular response to xenobiotic stimulus
E	0071548	biological_process	response to dexamethasone
E	0097421	biological_process	liver regeneration
E	1902065	biological_process	response to L-glutamate
E	1902990	biological_process	mitotic telomere maintenance via semi-conservative replication
F	0000122	biological_process	negative regulation of transcription by RNA polymerase II
F	0000307	cellular_component	cyclin-dependent protein kinase holoenzyme complex
F	0000701	molecular_function	purine-specific mismatch base pair DNA N-glycosylase activity
F	0000781	cellular_component	chromosome, telomeric region
F	0000785	cellular_component	chromatin
F	0001673	cellular_component	male germ cell nucleus
F	0003677	molecular_function	DNA binding
F	0003682	molecular_function	chromatin binding
F	0003684	molecular_function	damaged DNA binding
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005652	cellular_component	nuclear lamina
F	0005654	cellular_component	nucleoplasm
F	0005657	cellular_component	replication fork
F	0005813	cellular_component	centrosome
F	0006260	biological_process	DNA replication
F	0006272	biological_process	leading strand elongation
F	0006275	biological_process	regulation of DNA replication
F	0006281	biological_process	DNA repair
F	0006287	biological_process	base-excision repair, gap-filling
F	0006298	biological_process	mismatch repair
F	0006325	biological_process	chromatin organization
F	0006974	biological_process	DNA damage response
F	0006979	biological_process	response to oxidative stress
F	0007507	biological_process	heart development
F	0016604	cellular_component	nuclear body
F	0019899	molecular_function	enzyme binding
F	0019985	biological_process	translesion synthesis
F	0030331	molecular_function	nuclear estrogen receptor binding
F	0030337	molecular_function	DNA polymerase processivity factor activity
F	0030855	biological_process	epithelial cell differentiation
F	0030894	cellular_component	replisome
F	0030971	molecular_function	receptor tyrosine kinase binding
F	0031297	biological_process	replication fork processing
F	0032139	molecular_function	dinucleotide insertion or deletion binding
F	0032355	biological_process	response to estradiol
F	0032405	molecular_function	MutLalpha complex binding
F	0033993	biological_process	response to lipid
F	0034644	biological_process	cellular response to UV
F	0035035	molecular_function	histone acetyltransferase binding
F	0042802	molecular_function	identical protein binding
F	0043596	cellular_component	nuclear replication fork
F	0043626	cellular_component	PCNA complex
F	0044849	biological_process	estrous cycle
F	0044877	molecular_function	protein-containing complex binding
F	0045739	biological_process	positive regulation of DNA repair
F	0045740	biological_process	positive regulation of DNA replication
F	0046686	biological_process	response to cadmium ion
F	0070062	cellular_component	extracellular exosome
F	0070182	molecular_function	DNA polymerase binding
F	0070301	biological_process	cellular response to hydrogen peroxide
F	0070557	cellular_component	PCNA-p21 complex
F	0071466	biological_process	cellular response to xenobiotic stimulus
F	0071548	biological_process	response to dexamethasone
F	0097421	biological_process	liver regeneration
F	1902065	biological_process	response to L-glutamate
F	1902990	biological_process	mitotic telomere maintenance via semi-conservative replication
G	0000122	biological_process	negative regulation of transcription by RNA polymerase II
G	0000307	cellular_component	cyclin-dependent protein kinase holoenzyme complex
G	0000701	molecular_function	purine-specific mismatch base pair DNA N-glycosylase activity
G	0000781	cellular_component	chromosome, telomeric region
G	0000785	cellular_component	chromatin
G	0001673	cellular_component	male germ cell nucleus
G	0003677	molecular_function	DNA binding
G	0003682	molecular_function	chromatin binding
G	0003684	molecular_function	damaged DNA binding
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005652	cellular_component	nuclear lamina
G	0005654	cellular_component	nucleoplasm
G	0005657	cellular_component	replication fork
G	0005813	cellular_component	centrosome
G	0006260	biological_process	DNA replication
G	0006272	biological_process	leading strand elongation
G	0006275	biological_process	regulation of DNA replication
G	0006281	biological_process	DNA repair
G	0006287	biological_process	base-excision repair, gap-filling
G	0006298	biological_process	mismatch repair
G	0006325	biological_process	chromatin organization
G	0006974	biological_process	DNA damage response
G	0006979	biological_process	response to oxidative stress
G	0007507	biological_process	heart development
G	0016604	cellular_component	nuclear body
G	0019899	molecular_function	enzyme binding
G	0019985	biological_process	translesion synthesis
G	0030331	molecular_function	nuclear estrogen receptor binding
G	0030337	molecular_function	DNA polymerase processivity factor activity
G	0030855	biological_process	epithelial cell differentiation
G	0030894	cellular_component	replisome
G	0030971	molecular_function	receptor tyrosine kinase binding
G	0031297	biological_process	replication fork processing
G	0032139	molecular_function	dinucleotide insertion or deletion binding
G	0032355	biological_process	response to estradiol
G	0032405	molecular_function	MutLalpha complex binding
G	0033993	biological_process	response to lipid
G	0034644	biological_process	cellular response to UV
G	0035035	molecular_function	histone acetyltransferase binding
G	0042802	molecular_function	identical protein binding
G	0043596	cellular_component	nuclear replication fork
G	0043626	cellular_component	PCNA complex
G	0044849	biological_process	estrous cycle
G	0044877	molecular_function	protein-containing complex binding
G	0045739	biological_process	positive regulation of DNA repair
G	0045740	biological_process	positive regulation of DNA replication
G	0046686	biological_process	response to cadmium ion
G	0070062	cellular_component	extracellular exosome
G	0070182	molecular_function	DNA polymerase binding
G	0070301	biological_process	cellular response to hydrogen peroxide
G	0070557	cellular_component	PCNA-p21 complex
G	0071466	biological_process	cellular response to xenobiotic stimulus
G	0071548	biological_process	response to dexamethasone
G	0097421	biological_process	liver regeneration
G	1902065	biological_process	response to L-glutamate
G	1902990	biological_process	mitotic telomere maintenance via semi-conservative replication

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue ZN A 1201

Chain	Residue
A	CYS1012
A	CYS1015
A	CYS1026
A	CYS1029

---

site_id	AC2
Number of Residues	6
Details	binding site for residue SF4 A 1202

Chain	Residue
A	PHE1079
A	CYS1058
A	CYS1061
A	CYS1071
A	CYS1076
A	ILE1078

---

site_id	AC3
Number of Residues	10
Details	binding site for residue TTP T 101

Chain	Residue
A	PHE603
A	SER604
A	SER605
A	LEU606
A	TYR607
A	ARG667
A	LYS694
A	ASN698
A	ASP757
P	DOC25

---

site_id	AC4
Number of Residues	8
Details	binding site for Di-nucleotide DG P 24 and DOC P 25

Chain	Residue
A	ASP755
A	THR756
A	LYS807
P	DT23
T	DG1
T	DC2
T	DA3
T	TTP101

---

Functional Information from PROSITE/UniProt

site_id	PS00116
Number of Residues	9
Details	DNA_POLYMERASE_B DNA polymerase family B signature. YGDTDSVMC

Chain	Residue	Details
A	TYR753-CYS761

---

site_id	PS00293
Number of Residues	19
Details	PCNA_2 Proliferating cell nuclear antigen signature 2. RCDRnlaMgvnLtSMsKIL

Chain	Residue	Details
E	ARG61-LEU79

---

site_id	PS01251
Number of Residues	24
Details	PCNA_1 Proliferating cell nuclear antigen signature 1. GVnLqSMDsSHVsLVqLtLrsegF

Chain	Residue	Details
E	GLY34-PHE57

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	17
Details	Zinc finger: {"description":"CysA-type"}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	18
Details	Motif: {"description":"CysB motif"}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	8
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	8
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	1
Details	Modified residue: {"description":"N-acetylmethionine","evidences":[{"source":"PubMed","id":"22223895","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"22814378","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	Modified residue: {"description":"N-acetylalanine","evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAR-2009","submissionDatabase":"UniProtKB","authors":["Bienvenut W.V.","Waridel P.","Quadroni M."]}},{"source":"PubMed","id":"22223895","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	57
Details	DNA binding: {"evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	279
Details	Region: {"description":"Interaction with NUDT15","evidences":[{"source":"PubMed","id":"19419956","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	3
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19419956","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	9
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	3
Details	Modified residue: {"description":"Phosphotyrosine; by EGFR","evidences":[{"source":"PubMed","id":"17115032","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38459011","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	3
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"PubMed","id":"17108083","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17130289","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---