5NM5

Tubulin Darpin room-temperature structure in complex with Colchicine determined by serial millisecond crystallography

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	Tubulin nucleotide-binding domain-like	8034386	3001758	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tubulin C-terminal domain-like	8034387	3001732	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tubulin C-terminal domain-like	8034385	3001732	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tubulin nucleotide-binding domain-like	8034383	3001758	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	Tubulin_C	e5nm5B1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: Tubulin C-terminal domain-like (From Topology)	T: Tubulin C-terminal domain-like	F: Tubulin_C	ECOD (1.6)
B	Tubulin	e5nm5B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Tubulin nucleotide-binding domain-like	F: Tubulin	ECOD (1.6)
A	Tubulin_C	e5nm5A1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: Tubulin C-terminal domain-like (From Topology)	T: Tubulin C-terminal domain-like	F: Tubulin_C	ECOD (1.6)
A	Tubulin	e5nm5A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Tubulin nucleotide-binding domain-like	F: Tubulin	ECOD (1.6)
C [auth F]	Ank_2	e5nm5F1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Ankyrin repeat (From Topology)	T: Ankyrin repeat	F: Ank_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.1440	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Tubulin/FtsZ, GTPase domain	CATH (4.3.0)
B	3.30.1330.20	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
B	1.10.287.600	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
A	3.40.50.1440	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Tubulin/FtsZ, GTPase domain	CATH (4.3.0)
A	3.30.1330.20	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
A	1.10.287.600	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
C [auth F]	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF00091	Tubulin/FtsZ family, GTPase domain (Tubulin)	Tubulin/FtsZ family, GTPase domain	This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ...	This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ and tubulin are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules.	Domain
B	PF03953	Tubulin C-terminal domain (Tubulin_C)	Tubulin C-terminal domain	This family includes the tubulin alpha, beta and gamma chains. Members of this family are involved in polymer formation. Tubulins are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tub ...	This family includes the tubulin alpha, beta and gamma chains. Members of this family are involved in polymer formation. Tubulins are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules. (The FtsZ GTPases have been split into their won family).	Domain
A	PF00091	Tubulin/FtsZ family, GTPase domain (Tubulin)	Tubulin/FtsZ family, GTPase domain	This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ...	This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ and tubulin are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules.	Domain
A	PF03953	Tubulin C-terminal domain (Tubulin_C)	Tubulin C-terminal domain	This family includes the tubulin alpha, beta and gamma chains. Members of this family are involved in polymer formation. Tubulins are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tub ...	This family includes the tubulin alpha, beta and gamma chains. Members of this family are involved in polymer formation. Tubulins are GTPases. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules. (The FtsZ GTPases have been split into their won family).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Tubulin beta-2B chain	protein heterodimerization activity protein binding binding protein dimerization activity structural constituent of cytoskeleton structural molecule activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding protein heterodimerization activity protein binding binding protein dimerization activity structural constituent of cytoskeleton structural molecule activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding metal ion binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	cellular process cell cycle mitotic cell cycle multicellular organismal process axonogenesis regulation of cellular process response to stimulus cell projection organization neuron projection development multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis taxis cellular process cell cycle mitotic cell cycle multicellular organismal process axonogenesis regulation of cellular process response to stimulus cell projection organization neuron projection development multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis taxis regulation of axon guidance cell differentiation anatomical structure development positive regulation of cell projection organization system development developmental process chemotaxis regulation of biological process regulation of cell projection organization response to external stimulus nervous system development generation of neurons regulation of response to stimulus response to chemical regulation of locomotion regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization cellular developmental process regulation of response to external stimulus plasma membrane bounded cell projection morphogenesis positive regulation of biological process cell development cell morphogenesis cellular component organization neurogenesis positive regulation of neuron projection development positive regulation of axon guidance cellular component organization or biogenesis locomotion positive regulation of cellular process plasma membrane bounded cell projection organization biological regulation axon guidance axon development regulation of chemotaxis cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron projection guidance neuron development regulation of plasma membrane bounded cell projection organization organelle organization microtubule cytoskeleton organization microtubule-based process cytoskeleton organization	cellular anatomical structure intracellular anatomical structure cytoplasm polymeric cytoskeletal fiber intracellular membraneless organelle intracellular organelle cytoskeleton organelle membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton
A	Tubulin alpha-1B chain	structural constituent of cytoskeleton structural molecule activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding structural constituent of cytoskeleton structural molecule activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding metal ion binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	cellular process cell cycle mitotic cell cycle cellular component organization organelle organization microtubule cytoskeleton organization microtubule-based process cellular component organization or biogenesis cytoskeleton organization	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol polymeric cytoskeletal fiber intracellular membraneless organelle intracellular organelle cytoskeleton organelle membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol polymeric cytoskeletal fiber intracellular membraneless organelle intracellular organelle cytoskeleton organelle membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton
C [auth F]	Designed Ankyrin Repeat Protein (DARPIN) D1	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR003008	Tubulin/FtsZ, GTPase domain	Domain
B	IPR008280	Tubulin/FtsZ, C-terminal	Homologous Superfamily
B	IPR037103	Tubulin/FtsZ-like, C-terminal domain	Homologous Superfamily
B	IPR017975	Tubulin, conserved site	Conserved Site
B	IPR000217	Tubulin	Family
B	IPR023123	Tubulin, C-terminal	Homologous Superfamily
B	IPR002453	Beta tubulin	Family
B	IPR013838	Beta tubulin, autoregulation binding site	Binding Site
B	IPR018316	Tubulin/FtsZ, 2-layer sandwich domain	Domain
B	IPR036525	Tubulin/FtsZ, GTPase domain superfamily	Homologous Superfamily
A	IPR003008	Tubulin/FtsZ, GTPase domain	Domain
A	IPR008280	Tubulin/FtsZ, C-terminal	Homologous Superfamily
A	IPR037103	Tubulin/FtsZ-like, C-terminal domain	Homologous Superfamily
A	IPR017975	Tubulin, conserved site	Conserved Site
A	IPR002452	Alpha tubulin	Family
A	IPR000217	Tubulin	Family
A	IPR023123	Tubulin, C-terminal	Homologous Superfamily
A	IPR018316	Tubulin/FtsZ, 2-layer sandwich domain	Domain
A	IPR036525	Tubulin/FtsZ, GTPase 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.