4YD1

Ternary complex of human DNA Polymerase Mu with 2-nt gapped DNA substrate and an incoming nonhydrolyzable dUMPNPP

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DNA_pol_lambd_f	e4yd1A1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: DNA_pol_lambd_f	ECOD (1.6)
A	HHH_8	e4yd1A3	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_8	ECOD (1.6)
A	DNA_pol_B_palm	e4yd1A2	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: DNA_pol_B_palm	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.150.110	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
A	3.30.210.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF14716	Helix-hairpin-helix domain (HHH_8)	Helix-hairpin-helix domain	-	Domain
A	PF14791	DNA polymerase beta thumb (DNA_pol_B_thumb)	DNA polymerase beta thumb	-	Family
A	PF14792	DNA polymerase beta palm (DNA_pol_B_palm)	DNA polymerase beta palm	The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain [1].	Domain
A	PF10391	Fingers domain of DNA polymerase lambda (DNA_pol_lambd_f)	Fingers domain of DNA polymerase lambda	DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the centr ...	DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA-directed DNA/RNA polymerase mu	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding cation binding ion binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	nucleobase-containing compound metabolic process DNA recombination metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus double-strand break repair response to stimulus double-strand break repair via nonhomologous end joining cellular response to stress DNA damage response response to stress nucleobase-containing compound metabolic process DNA recombination metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus double-strand break repair response to stimulus double-strand break repair via nonhomologous end joining cellular response to stress DNA damage response response to stress cellular process DNA repair	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
C [auth P]	DNA (5'-D(CPGPTPA)-3')	-	-	-
B [auth T]	DNA (5'-D(CPGPGPCPAPAPTPAPCPG)-3')	-	-	-
D	DNA (5'-D(PGPCPCPG)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR028207	DNA polymerase beta, palm domain	Domain
A	IPR037160	DNA polymerase, thumb domain superfamily	Homologous Superfamily
A	IPR019843	DNA polymerase family X, binding site	Binding Site
A	IPR022312	DNA polymerase family X	Family
A	IPR010996	DNA polymerase beta-like, N-terminal domain	Domain
A	IPR001726	DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu	Family
A	IPR029398	DNA polymerase beta, thumb domain	Domain
A	IPR018944	DNA polymerase lambda, fingers domain	Domain
A	IPR043519	Nucleotidyltransferase superfamily	Homologous Superfamily
A	IPR001357	BRCT domain	Domain
A	IPR027421	DNA polymerase lambda lyase domain superfamily	Homologous Superfamily
A	IPR036420	BRCT domain superfamily	Homologous Superfamily
A	IPR002054	DNA-directed DNA polymerase X	Domain
A	IPR027249	DNA-directed DNA/RNA polymerase mu	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9NP87	carpal tunnel syndrome xeroderma pigmentosum

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.