4NIK | pdb_00004nik

Structure of human Gankyrin in complex to the single chain antibody F5

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
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)
A	SCOP2B Superfamily	Ankyrin repeat	8057705	3000154	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		e4nikB1	A: DP domain	X: DP domain	H: DP domain	T: DUF5074	F:	ECOD (20:10:01)
A		e4nikA1	A: DP domain	X: DP domain	H: DP domain	T: DUF5074	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B	F5, anti-PSMD10 (gankyrin)	SCFV-HEAVY-LAMBDA	Homo sapiens (human)	IGHV3-2101, IGHV3-2102, IGHV3-2104, IGHV3-2103, IGHJ401, IGHJ402, IGHJ403, IGLV2-1401, IGLJ201, IGLJ302, IGLJ3*01	V-DOMAIN VH, V-DOMAIN V-LAMBDA	IG	SCFV-HEAVY-LAMBDA	IMGT (202609-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF12796	Ankyrin repeats (3 copies) (Ank_2)	Ankyrin repeats (3 copies)	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Single-chain Fv fragment antibody	-	-	-
A	26S proteasome non-ATPase regulatory subunit 10	transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding	regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis positive regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death cellular response to stimulus response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of cellular response to stress regulation of signal transduction DNA damage response, signal transduction by p53 class mediator intracellular signal transduction negative regulation of cell communication cell communication cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress regulation of signal transduction by p53 class mediator negative regulation of DNA damage response, signal transduction by p53 class mediator signal transduction regulation of DNA damage response, signal transduction by p53 class mediator negative regulation of signal transduction by p53 class mediator regulation of signaling negative regulation of response to stimulus signal transduction by p53 class mediator negative regulation of signal transduction regulation of response to stimulus DNA damage response regulation of cell communication signal transduction in response to DNA damage regulation of protein modification process positive regulation of protein metabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process protein ubiquitination positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process macromolecule modification metabolic process macromolecule metabolic process post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal positive regulation of proteasomal protein catabolic process catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process positive regulation of protein serine/threonine kinase activity positive regulation of cyclin-dependent protein serine/threonine kinase activity regulation of cyclin-dependent protein serine/threonine kinase activity phosphate-containing compound metabolic process cell cycle phosphorus metabolic process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of molecular function positive regulation of kinase activity regulation of kinase activity regulation of protein serine/threonine kinase activity regulation of phosphorus metabolic process regulation of protein phosphorylation positive regulation of cyclin-dependent protein kinase activity positive regulation of molecular function positive regulation of protein kinase activity regulation of cell cycle positive regulation of catalytic activity regulation of protein kinase activity positive regulation of cell cycle regulation of phosphorylation cellular component biogenesis proteasome assembly cellular component assembly protein-containing complex organization protein-containing complex assembly proteasome regulatory particle assembly intracellular signaling cassette regulation of MAPK cascade MAPK cascade negative regulation of MAPK cascade apoptotic mitochondrial changes regulation of release of cytochrome c from mitochondria negative regulation of release of cytochrome c from mitochondria negative regulation of apoptotic signaling pathway mitochondrion organization negative regulation of cellular component organization regulation of organelle organization apoptotic signaling pathway organelle organization release of cytochrome c from mitochondria negative regulation of organelle organization regulation of mitochondrion organization regulation of apoptotic signaling pathway RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process	membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection intracellular anatomical structure cytoplasm cytosol ciliary tip sperm principal piece 9+2 motile cilium sperm flagellum motile cilium membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection intracellular anatomical structure cytoplasm cytosol ciliary tip sperm principal piece 9+2 motile cilium sperm flagellum motile cilium intracellular organelle perinuclear theca cytoskeleton perinuclear region of cytoplasm membraneless organelle intracellular membraneless organelle sperm midpiece cell periphery external encapsulating structure glycocalyx sperm glycocalyx microtubule cytoskeleton protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A	IPR002110	Ankyrin repeat	Repeat
A	IPR051637	Ankyrin repeat domain-containing protein 49	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O75832	breast cancer ovarian cancer intellectual disability plasma cell myeloma osteosarcoma psoriasis

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.