5W2C | pdb_00005w2c

Structure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and incoming dAMPNPP

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Lesion bypass DNA polymerase (Y-family), little finger domain	8040087	3000579	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ta1206-like	8055761	3001431	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8040088	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Lesion bypass DNA polymerase (Y-family), little finger domain	8040087	3000579	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ta1206-like	8055761	3001431	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8040088	3001272	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e5w2cB1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: Jacalin	F:	ECOD (20:10:01)
A		e5w2cA1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: Jacalin	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.150.810	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
B	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
B	3.40.1170.60	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I		CATH (4.3.0)
B	3.30.1490.100	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
A	1.10.150.810	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
A	3.40.1170.60	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I		CATH (4.3.0)
A	3.30.1490.100	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00817	impB/mucB/samB family (IMS)	impB/mucB/samB family	-	Family
A, B	PF11799	impB/mucB/samB family C-terminal domain (IMS_C)	impB/mucB/samB family C-terminal domain	These proteins are involved in UV protection (Swiss).	Domain
A, B	PF11798	IMS family HHH motif (IMS_HHH)	IMS family HHH motif	-	Motif

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, F [auth T]	DNA (5'-D(CPTPAPTP(LDG)PTPCPGPAPTPCPCP*G)-3')	-	-	-
C, E [auth P]	DNA (5'-D(PCPGPGPAPTPCPGPAP*C)-3')	-	-	-
A, B	DNA polymerase kappa	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 cation binding transition metal ion binding zinc ion binding ion binding binding metal 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 cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding DNA binding damaged DNA binding nucleic acid binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process nucleobase-containing compound biosynthetic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process translesion synthesis DNA damage tolerance DNA synthesis involved in DNA replication error-prone translesion synthesis response to light stimulus cellular response to radiation response to UV cellular response to environmental stimulus cellular response to light stimulus response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV DNA repair nucleotide-excision repair, DNA gap filling nucleotide-excision repair	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear body intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear body intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle nuclear lumen site of DNA damage chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001126	UmuC domain	Domain
A, B	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B	IPR036775	DNA polymerase, Y-family, little finger domain superfamily	Homologous Superfamily
A, B	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B	IPR050116	DNA polymerase type-Y	Family
A, B	IPR022880	DNA polymerase IV	Family
A, B	IPR017961	DNA polymerase, Y-family, little finger domain	Domain
A, B	IPR006642	Rad18, zinc finger UBZ4-type	Domain
A, B	IPR024728	DNA polymerase type-Y, HhH motif	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9UBT6	glioblastoma giant cell glioblastoma cystic fibrosis osteosarcoma primitive neuroectodermal tumor sinusitis familial prostate carcinoma juvenile dermatomyositis ovarian cancer prostate cancer Micronuclei, Chromosome-Defective Pick disease rheumatoid arthritis

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.