2D5G | pdb_00002d5g

Structure of ubiquitin fold protein R767E mutant

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d2d5gf1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	DIX domain	Axin 1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
E	d2d5ge1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	DIX domain	Axin 1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D	d2d5gd1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	DIX domain	Axin 1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C	d2d5gc1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	DIX domain	Axin 1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d2d5gb1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	DIX domain	Axin 1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d2d5ga1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	DIX domain	Axin 1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Ubiquitin-like	8033375	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8033375	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8033375	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8033375	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8033375	3000157	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ubiquitin-like	8033375	3000157	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)
F	DIX	e2d5gF1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)
E	DIX	e2d5gE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)
D	DIX	e2d5gD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)
C	DIX	e2d5gC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)
B	DIX	e2d5gB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)
A	DIX	e2d5gA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
E	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
D	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
C	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
B	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
A	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00778	DIX domain (DIX)	DIX domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Axin-1	SMAD binding protein binding binding R-SMAD binding ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity I-SMAD binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding enzyme regulator activity protein serine/threonine kinase activator activity SMAD binding protein binding binding R-SMAD binding ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity I-SMAD binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity identical protein binding p53 binding protein domain specific binding signaling receptor binding armadillo repeat domain binding protein serine/threonine kinase binding kinase binding protein kinase binding protein homodimerization activity protein dimerization activity beta-catenin binding	cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process cell surface receptor signaling pathway response to stimulus regulation of Wnt signaling pathway signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway biological regulation regulation of signal transduction cell communication regulation of response to stimulus cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process cell surface receptor signaling pathway response to stimulus regulation of Wnt signaling pathway signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway biological regulation regulation of signal transduction cell communication regulation of response to stimulus regulation of cell communication cellular process signal transduction Wnt signaling pathway developmental process multicellular organism development multicellular organismal process dorsal/ventral pattern formation dorsal/ventral axis specification anatomical structure development pattern specification process axis specification regionalization localization cellular localization nucleocytoplasmic transport transport nuclear transport establishment of localization in cell intracellular transport establishment of localization apoptotic process cell death programmed cell death negative regulation of signaling negative regulation of biological process negative regulation of cell communication negative regulation of Wnt signaling pathway negative regulation of cellular process negative regulation of response to stimulus negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway transcription elongation by RNA polymerase II RNA metabolic process negative regulation of transcription elongation by RNA polymerase II regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of DNA-templated transcription elongation negative regulation of DNA-templated transcription regulation of transcription elongation by RNA polymerase II negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process negative regulation of DNA-templated transcription, elongation regulation of gene expression DNA-templated transcription elongation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process catabolic process protein catabolic process protein metabolic process macromolecule catabolic process cellular developmental process cell differentiation cell development positive regulation of proteasomal protein catabolic process positive regulation of protein metabolic process proteolysis involved in protein catabolic process positive regulation of biological process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process proteolysis positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of protein metabolic process proteasomal protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process positive regulation of proteolysis 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 embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development anatomical structure morphogenesis post-anal tail morphogenesis hemoglobin metabolic process negative regulation of protein metabolic process positive regulation of cell communication positive regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade positive regulation of signaling protein polyubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal epigenetic programming of gene expression epigenetic programming in the zygotic pronuclei epigenetic regulation of gene expression cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly beta-catenin destruction complex assembly system process sensory perception nervous system process sensory perception of sound sensory perception of mechanical stimulus adult walking behavior adult locomotory behavior behavior adult behavior locomotory behavior walking behavior response to chemical response to oxygen-containing compound response to quercetin response to flavonoid fat cell differentiation regulation of developmental process negative regulation of developmental process regulation of cell differentiation negative regulation of fat cell differentiation negative regulation of cell differentiation regulation of fat cell differentiation embryonic skeletal joint development embryonic organ morphogenesis embryonic morphogenesis animal organ development embryonic skeletal joint morphogenesis skeletal system development embryonic skeletal system development animal organ morphogenesis skeletal system morphogenesis embryonic organ development embryonic skeletal system morphogenesis system development cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of transforming growth factor beta receptor signaling pathway cellular response to endogenous stimulus enzyme-linked receptor protein signaling pathway regulation of cellular response to transforming growth factor beta stimulus response to endogenous stimulus positive regulation of transforming growth factor beta receptor signaling pathway regulation of cellular response to growth factor stimulus positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of cellular response to transforming growth factor beta stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway response to growth factor transforming growth factor beta receptor superfamily signaling pathway formation of primary germ layer mesoderm morphogenesis tissue development gastrulation axial mesoderm development tissue morphogenesis axial mesoderm formation anatomical structure formation involved in morphogenesis axial mesoderm morphogenesis mesoderm formation mesoderm development head development multicellular organismal-level homeostasis homeostatic process immune system process homeostasis of number of cells myeloid cell homeostasis erythrocyte homeostasis regulation of protein modification process regulation of protein ubiquitination positive regulation of post-translational protein modification positive regulation of protein modification process regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification organelle organization microtubule cytoskeleton organization microtubule-based process cytoplasmic microtubule organization supramolecular fiber organization cytoskeleton organization negative regulation of gene expression	cellular anatomical structure intracellular anatomical structure cytoplasm perinuclear region of cytoplasm cell periphery cell cortex plasma membrane membrane protein-containing complex catalytic complex beta-catenin destruction complex intracellular protein-containing complex intracellular organelle cytoskeleton cellular anatomical structure intracellular anatomical structure cytoplasm perinuclear region of cytoplasm cell periphery cell cortex plasma membrane membrane protein-containing complex catalytic complex beta-catenin destruction complex intracellular protein-containing complex intracellular organelle cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton Wnt signalosome membrane-bounded organelle cytoplasmic vesicle intracellular vesicle intracellular membrane-bounded organelle vesicle synapse cell junction lateral plasma membrane nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR016137	RGS domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036305	RGS domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR032101	Axin-1/2, tankyrase-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR044926	RGS, subdomain 2	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR038207	DIX domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR024066	RGS, subdomain 1/3	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR043581	Axin-like	Family
A, B, C, D, E A, B, C, D, E, F	IPR014936	Axin beta-catenin binding	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001158	DIX domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR029071	Ubiquitin-like domain superfamily	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.