3ZVM | pdb_00003zvm

The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8019137	3002021	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HAD-like	8019133	3001890	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HAD-like	8019133	3001890	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8019137	3002021	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	AAA_33	e3zvmB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_33	ECOD (1.6)
B	PNK3P	e3zvmB2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: PNK3P	ECOD (1.6)
A	AAA_33	e3zvmA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_33	ECOD (1.6)
A	PNK3P	e3zvmA2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: HAD-like	F: PNK3P	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF13671	AAA domain (AAA_33)	AAA domain	This family of domains contain only a P-loop motif, that is characteristic of the AAA superfamily. Many of the proteins in this family are just short fragments so there is no Walker B motif.	Domain
A, B	PF08645	Polynucleotide kinase 3 phosphatase (PNK3P)	Polynucleotide kinase 3 phosphatase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth E], D [auth F]	5'-D(GPTPCPAP*CP)-3'	-	-	-
A, B	BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity polynucleotide 3'-phosphatase activity ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity nucleobase-containing compound kinase activity polynucleotide 5'-hydroxyl-kinase activity kinase activity ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity transferase activity ATP-dependent polynucleotide 5'-hydroxyl-kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process protein polyubiquitination primary metabolic process protein K63-linked ubiquitination protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process protein polyubiquitination primary metabolic process protein K63-linked ubiquitination protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal double-strand break repair double-strand break repair via nonhomologous end joining DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA repair	intracellular organelle site of double-strand break cellular anatomical structure intracellular anatomical structure organelle membraneless organelle site of DNA damage intracellular membraneless organelle chromosome cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex intracellular organelle site of double-strand break cellular anatomical structure intracellular anatomical structure organelle membraneless organelle site of DNA damage intracellular membraneless organelle chromosome cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex SCF ubiquitin ligase complex transferase complex intracellular protein-containing complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR006549	HAD-superfamily hydrolase,subfamily IIIA	Domain
A, B	IPR023214	HAD superfamily	Homologous Superfamily
A, B	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
A, B	IPR006551	Polynucleotide 3'-phosphatase	Domain
A, B	IPR013954	Polynucleotide kinase 3 phosphatase	Family
A, B	IPR041388	PNK, FHA domain	Domain
A, B	IPR036412	HAD-like superfamily	Homologous Superfamily
A, B	IPR006550	Bifunctional polynucleotide phosphatase/kinase PNKP	Family
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.