6CO2 | pdb_00006co2

Structure of an engineered protein (NUDT16TI) in complex with 53BP1 Tudor domains

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d6co2d2	All beta proteins	SH3-like barrel	Tudor/PWWP/MBT	Tudor domain	p53-binding protein 1, 53BP1, C-terminal domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6co2d1	All beta proteins	SH3-like barrel	Tudor/PWWP/MBT	Tudor domain	p53-binding protein 1, 53BP1, N-terminal domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6co2c2	All beta proteins	SH3-like barrel	Tudor/PWWP/MBT	Tudor domain	p53-binding protein 1, 53BP1, C-terminal domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6co2c1	All beta proteins	SH3-like barrel	Tudor/PWWP/MBT	Tudor domain	p53-binding protein 1, 53BP1, N-terminal domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8041640	3000404	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8041642	3000404	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8041640	3000404	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8041642	3000404	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nudix	8086554	3000098	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nudix	8086554	3000098	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)
D	53-BP1_Tudor_C	e6co2D2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: 53-BP1_Tudor_C	ECOD (1.6)
D	53-BP1_Tudor_N	e6co2D1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: 53-BP1_Tudor_N	ECOD (1.6)
C	53-BP1_Tudor_C	e6co2C2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: 53-BP1_Tudor_C	ECOD (1.6)
C	53-BP1_Tudor_N	e6co2C1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: 53-BP1_Tudor_N	ECOD (1.6)
B	NUDIX_3	e6co2B1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_3	ECOD (1.6)
A	NUDIX_3	e6co2A1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
D	2.30.30.30	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
C	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
C	2.30.30.30	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
B	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)
A	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF22327	U8 snoRNA-decapping enzyme-like (Nudt16-like)	U8 snoRNA-decapping enzyme-like	This entry represents the NUDIX hydrolase domain of U8 snoRNA -decapping enzyme from Xenopus laevis (Nudt16) and similar proteins from animals and bacteria. Nudt16 was initially described as an RNA-binding and decapping enzyme but it was later report ...	This entry represents the NUDIX hydrolase domain of U8 snoRNA -decapping enzyme from Xenopus laevis (Nudt16) and similar proteins from animals and bacteria. Nudt16 was initially described as an RNA-binding and decapping enzyme but it was later reported to be specialised in the removal of hazardous (deoxy)inosine diphosphate from the nucleotide pool. It adopts a canonical NUDIX fold, an alpha-beta-alpha sandwich constituted by two beta-sheets whose strands interact in a way that could also be described as a single extended beta-sheet [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	TP53-binding protein 1	p53 binding protein binding binding histone reader activity histone H4K20me2 reader activity histone H4 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity histone binding transcription regulator activity transcription coregulator activity ubiquitin-modified protein reader activity ubiquitin-modified histone reader activity p53 binding protein binding binding histone reader activity histone H4K20me2 reader activity histone H4 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity histone binding transcription regulator activity transcription coregulator activity ubiquitin-modified protein reader activity ubiquitin-modified histone reader activity ubiquitin-like protein reader activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding transcription coactivator activity sequence-specific DNA binding DNA binding nucleic acid binding telomeric DNA binding damaged DNA binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of DNA recombination regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress negative regulation of biological process regulation of primary metabolic process negative regulation of DNA repair nucleobase-containing compound metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of DNA recombination regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress negative regulation of biological process regulation of primary metabolic process negative regulation of DNA repair nucleobase-containing compound metabolic process regulation of response to stress negative regulation of double-strand break repair negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process recombinational repair regulation of nucleobase-containing compound metabolic process negative regulation of double-strand break repair via homologous recombination double-strand break repair via homologous recombination DNA repair negative regulation of macromolecule metabolic process double-strand break repair regulation of biological process negative regulation of response to stimulus negative regulation of metabolic process DNA recombination biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of DNA repair regulation of double-strand break repair via homologous recombination negative regulation of DNA recombination regulation of response to stimulus metabolic process negative regulation of DNA metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of leukocyte activation regulation of cell activation B cell activation involved in immune response positive regulation of macromolecule biosynthetic process multicellular organism development positive regulation of immune response regulation of immune system process positive regulation of macromolecule metabolic process system development positive regulation of DNA recombination positive regulation of immunoglobulin mediated immune response immune response immune effector process regulation of gene expression biosynthetic process positive regulation of DNA metabolic process B cell mediated immunity positive regulation of production of molecular mediator of immune response regulation of macromolecule biosynthetic process immunoglobulin production regulation of developmental process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains somatic cell DNA recombination positive regulation of lymphocyte activation somatic diversification of immunoglobulins involved in immune response somatic recombination of immunoglobulin gene segments positive regulation of biosynthetic process regulation of immunoglobulin mediated immune response positive regulation of isotype switching regulation of B cell activation leukocyte activation involved in immune response positive regulation of immune effector process positive regulation of cellular process positive regulation of immunoglobulin production production of molecular mediator of immune response regulation of isotype switching cell activation macromolecule biosynthetic process positive regulation of gene expression immune system process somatic diversification of immune receptors via germline recombination within a single locus regulation of lymphocyte activation multicellular organismal process regulation of immune effector process lymphocyte mediated immunity positive regulation of leukocyte mediated immunity cell activation involved in immune response positive regulation of developmental process positive regulation of cell activation positive regulation of metabolic process positive regulation of leukocyte activation anatomical structure development leukocyte mediated immunity somatic diversification of immune receptors positive regulation of adaptive immune response positive regulation of immune system process somatic recombination of immunoglobulin genes involved in immune response developmental process regulation of adaptive immune response regulation of B cell mediated immunity somatic diversification of immunoglobulins regulation of leukocyte mediated immunity positive regulation of multicellular organismal process regulation of immune response regulation of production of molecular mediator of immune response isotype switching immune system development positive regulation of lymphocyte mediated immunity immunoglobulin production involved in immunoglobulin-mediated immune response positive regulation of biological process lymphocyte activation positive regulation of B cell mediated immunity leukocyte activation positive regulation of response to stimulus regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of multicellular organismal process lymphocyte activation involved in immune response regulation of biosynthetic process B cell activation gene expression positive regulation of B cell activation adaptive immune response immunoglobulin mediated immune response regulation of immunoglobulin production regulation of lymphocyte mediated immunity double-strand break repair via classical nonhomologous end joining double-strand break repair via nonhomologous end joining localization protein localization to chromosome protein localization to organelle macromolecule localization protein localization to site of double-strand break intracellular protein localization positive regulation of cell communication positive regulation of signal transduction signaling positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of signal transduction regulation of programmed cell death regulation of intrinsic apoptotic signaling pathway intracellular signal transduction cell communication positive regulation of apoptotic signaling pathway regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator positive regulation of signal transduction by p53 class mediator signal transduction intrinsic apoptotic signaling pathway regulation of signaling positive regulation of programmed cell death regulation of apoptotic process positive regulation of intracellular signal transduction signal transduction by p53 class mediator cell death positive regulation of apoptotic process apoptotic signaling pathway regulation of cell communication intrinsic apoptotic signaling pathway by p53 class mediator positive regulation of intrinsic apoptotic signaling pathway apoptotic process regulation of intrinsic apoptotic signaling pathway by p53 class mediator programmed cell death regulation of apoptotic signaling pathway positive regulation of signaling response to X-ray cellular response to ionizing radiation cellular response to radiation cellular response to environmental stimulus cellular response to X-ray response to ionizing radiation response to radiation response to abiotic stimulus cellular response to abiotic stimulus positive regulation of DNA-templated transcription RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II DNA damage checkpoint signaling regulation of cell cycle phase transition negative regulation of cell cycle cell cycle phase transition negative regulation of cell cycle phase transition cell cycle regulation of cell cycle cell cycle process regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling signal transduction in response to DNA damage	protein-containing complex catalytic complex DNA repair complex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen protein-containing complex catalytic complex DNA repair complex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular membraneless organelle chromosome chromosomal region kinetochore membraneless organelle chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome replication fork site of double-strand break site of DNA damage nuclear body chromosome, telomeric region
A, B	NUDT16-Tudor-interacting (NUDT16TI)	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding RNA binding snoRNA binding nucleic acid binding pyrophosphatase activity dITP diphosphatase activity nucleoside triphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding RNA binding snoRNA binding nucleic acid binding pyrophosphatase activity dITP diphosphatase activity nucleoside triphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity nucleoside phosphate binding nucleotide binding heterocyclic compound binding manganese ion binding anion binding chloride ion binding magnesium ion binding mRNA binding phosphodiesterase decapping endonuclease activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity identical protein binding protein binding protein homodimerization activity protein dimerization activity RNA NAD-cap (NMN-forming) hydrolase activity dIDP phosphatase activity nucleoside diphosphate phosphatase activity peptidase activity catalytic activity, acting on a protein metallopeptidase activity exopeptidase activity metalloexopeptidase activity 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity IDP phosphatase activity	deoxyribonucleotide catabolic process catabolic process nucleoside triphosphate catabolic process purine nucleoside triphosphate catabolic process purine deoxyribonucleoside triphosphate metabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process deoxyribose phosphate catabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process deoxyribonucleotide metabolic process purine deoxyribonucleoside triphosphate catabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process deoxyribonucleotide catabolic process catabolic process nucleoside triphosphate catabolic process purine nucleoside triphosphate catabolic process purine deoxyribonucleoside triphosphate metabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process deoxyribose phosphate catabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process deoxyribonucleotide metabolic process purine deoxyribonucleoside triphosphate catabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleotide catabolic process deoxyribonucleoside triphosphate metabolic process nucleoside phosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process purine deoxyribonucleotide catabolic process carbohydrate derivative catabolic process 2'-deoxyribonucleotide metabolic process primary metabolic process purine-containing compound catabolic process deoxyribonucleoside triphosphate catabolic process nucleotide metabolic process purine-containing compound metabolic process nucleobase-containing compound catabolic process organophosphate metabolic process dITP catabolic process purine deoxyribonucleotide metabolic process metabolic process cellular process nucleoside triphosphate metabolic process NAD-cap decapping RNA metabolic process macromolecule metabolic process nucleic acid metabolic process RNA decapping ribonucleoprotein complex biogenesis regulation of cellular process negative regulation of biological process regulation of ribosome biogenesis rRNA processing regulation of primary metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of cellular component biogenesis macromolecule biosynthetic process regulation of rRNA processing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process negative regulation of ribosome biogenesis regulation of metabolic process negative regulation of rRNA processing negative regulation of RNA metabolic process macromolecule catabolic process RNA catabolic process mRNA catabolic process mRNA metabolic process nucleic acid catabolic process sno(s)RNA metabolic process sno(s)RNA catabolic process regulation of cell cycle process positive regulation of biological process positive regulation of cell cycle positive regulation of cell cycle process cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR047252	TP53-binding protein 1-like	Family
C, D	IPR014722	Large ribosomal subunit protein uL2, domain 2	Homologous Superfamily
C, D	IPR015125	Tumour suppressor p53-binding protein-1, Tudor domain	Domain
C, D	IPR001357	BRCT domain	Domain
C, D	IPR036420	BRCT domain superfamily	Homologous Superfamily
C, D	IPR047249	TP53-binding protein 1-like, first BRCT domain	Domain
C, D	IPR047250	TP53-binding protein 1-like, second BRCT domain	Domain
A, B	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A, B	IPR054754	U8 snoRNA-decapping enzyme NudT16	Family
A, B	IPR000086	NUDIX hydrolase domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: Q12888	astrocytic tumor lung carcinoma oligodendroglioma Pick disease cancer malignant ependymoma osteosarcoma lung cancer medulloblastoma ovarian cancer
A, B	Pharos: Q96DE0	Liver Cirrhosis, Experimental astrocytic tumor medulloblastoma pancreatic ductal adenocarcinoma endometriosis lung adenocarcinoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm large cell medulloblastoma malignant ependymoma osteosarcoma tuberculosis

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.