Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6P1H

Cryo-EM Structure of DNA Polymerase Delta Holoenzyme

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0003676	molecular_function	nucleic acid binding
A	0003677	molecular_function	DNA binding
A	0003887	molecular_function	DNA-directed DNA polymerase activity
A	0004527	molecular_function	exonuclease activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005657	cellular_component	replication fork
A	0005829	cellular_component	cytosol
A	0006259	biological_process	DNA metabolic process
A	0006260	biological_process	DNA replication
A	0006261	biological_process	DNA-templated DNA replication
A	0006278	biological_process	RNA-templated DNA biosynthetic process
A	0006287	biological_process	base-excision repair, gap-filling
A	0006297	biological_process	nucleotide-excision repair, DNA gap filling
A	0006303	biological_process	double-strand break repair via nonhomologous end joining
A	0008270	molecular_function	zinc ion binding
A	0008296	molecular_function	3'-5'-DNA exonuclease activity
A	0043137	biological_process	DNA replication, removal of RNA primer
A	0043231	cellular_component	intracellular membrane-bounded organelle
A	0043625	cellular_component	delta DNA polymerase complex
A	0045004	biological_process	DNA replication proofreading
A	0045005	biological_process	DNA-templated DNA replication maintenance of fidelity
A	0046872	molecular_function	metal ion binding
A	0051539	molecular_function	4 iron, 4 sulfur cluster binding
A	0060090	molecular_function	molecular adaptor activity
A	0071897	biological_process	DNA biosynthetic process
B	0003677	molecular_function	DNA binding
B	0003887	molecular_function	DNA-directed DNA polymerase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005829	cellular_component	cytosol
B	0006259	biological_process	DNA metabolic process
B	0006260	biological_process	DNA replication
B	0006271	biological_process	DNA strand elongation involved in DNA replication
B	0006272	biological_process	leading strand elongation
B	0006273	biological_process	lagging strand elongation
B	0006278	biological_process	RNA-templated DNA biosynthetic process
B	0006284	biological_process	base-excision repair
B	0006289	biological_process	nucleotide-excision repair
B	0006298	biological_process	mismatch repair
B	0006301	biological_process	postreplication repair
B	0008310	molecular_function	single-stranded DNA 3'-5' DNA exonuclease activity
B	0016035	cellular_component	zeta DNA polymerase complex
B	0043137	biological_process	DNA replication, removal of RNA primer
B	0043625	cellular_component	delta DNA polymerase complex
C	0000727	biological_process	double-strand break repair via break-induced replication
C	0003887	molecular_function	DNA-directed DNA polymerase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0006259	biological_process	DNA metabolic process
C	0006260	biological_process	DNA replication
C	0006272	biological_process	leading strand elongation
C	0006273	biological_process	lagging strand elongation
C	0006277	biological_process	DNA amplification
C	0006278	biological_process	RNA-templated DNA biosynthetic process
C	0006284	biological_process	base-excision repair
C	0006289	biological_process	nucleotide-excision repair
C	0008310	molecular_function	single-stranded DNA 3'-5' DNA exonuclease activity
C	0016035	cellular_component	zeta DNA polymerase complex
C	0042276	biological_process	error-prone translesion synthesis
C	0043137	biological_process	DNA replication, removal of RNA primer
C	0043625	cellular_component	delta DNA polymerase complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	7
Details	binding site for residue SF4 A 1101

Chain	Residue
A	CYS1056
A	CYS1059
A	CYS1069
A	ASN1071
A	CYS1074
A	ARG1080
B	LEU119

site_id	AC2
Number of Residues	13
Details	binding site for residue DCP A 1102

Chain	Residue
A	SER611
A	LEU612
A	TYR613
A	ARG674
A	LYS701
A	ASP764
A	CA1103
A	CA1104
P	DC30
T	DG5
T	DG6
A	PHE609
A	ASN610

site_id	AC3
Number of Residues	4
Details	binding site for residue CA A 1103

Chain	Residue
A	ASP608
A	PHE609
A	ASP764
A	DCP1102

site_id	AC4
Number of Residues	3
Details	binding site for residue CA A 1104

Chain	Residue
A	ASP764
A	DCP1102
A	HOH1225

site_id	AC5
Number of Residues	3
Details	binding site for residue CA A 1105

Chain	Residue
A	ASP608
A	ASN610
A	GLU800

site_id	AC6
Number of Residues	2
Details	binding site for residue CA A 1106

Chain	Residue
A	ASP321
A	ILE322

site_id	AC7
Number of Residues	1
Details	binding site for residue CA T 101

Chain	Residue
T	DG10

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	TYR760-VAL768

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:19779198

Chain	Residue	Details
C	THR223

site_id	SWS_FT_FI2
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:19779198

Chain	Residue	Details
A	CYS1056
A	CYS1059
A	CYS1069
A	CYS1074
C	SER230
A	CYS1012
A	CYS1024
A	CYS1027

site_id	SWS_FT_FI3
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:17330950, ECO:0007744\|PubMed:18407956, ECO:0007744\|PubMed:19779198

Chain	Residue	Details
A	SER30

site_id	SWS_FT_FI4
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:19779198

Chain	Residue	Details
A	SER37

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)