5XAF

Crystal structure of tubulin-stathmin-TTL-Compound Z1 complex

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	d5xaff1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	Tubulin tyrosine ligase (TTL) N-terminal domain-like	Tubulin tyrosine ligase (TTL) N-terminal domain	Chicken (Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)
F	d5xaff2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	Tubulin tyrosine ligase (TTL) C-terminal domain-like	Tubulin tyrosine ligase (TTL) C-terminal domain	Chicken (Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)
A	d5xafa1	Alpha and beta proteins (a/b)	Tubulin nucleotide-binding domain-like	Tubulin nucleotide-binding domain-like	Tubulin, GTPase domain	automated matches	Bovine (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
A	d5xafa2	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	Tubulin C-terminal domain-like	Tubulin, C-terminal domain	automated matches	Bovine (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
C	d5xafc1	Alpha and beta proteins (a/b)	Tubulin nucleotide-binding domain-like	Tubulin nucleotide-binding domain-like	Tubulin, GTPase domain	automated matches	Bovine (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
C	d5xafc2	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	Tubulin C-terminal domain-like	Tubulin, C-terminal domain	automated matches	Bovine (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
B	d5xafb1	Alpha and beta proteins (a/b)	Tubulin nucleotide-binding domain-like	Tubulin nucleotide-binding domain-like	Tubulin, GTPase domain	automated matches	Bovine (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
B	d5xafb2	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	Tubulin C-terminal domain-like	Tubulin, C-terminal domain	automated matches	Bovine (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
D	d5xafd1	Alpha and beta proteins (a/b)	Tubulin nucleotide-binding domain-like	Tubulin nucleotide-binding domain-like	Tubulin, GTPase domain	automated matches	Bovine (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
D	d5xafd2	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	Tubulin C-terminal domain-like	Tubulin, C-terminal domain	automated matches	Bovine (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)
E	d5xafe_	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Stathmin	Stathmin	Stathmin 4	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)
A	SCOP2B Superfamily	Tubulin nucleotide-binding domain-like	8034383	3001758	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tubulin C-terminal domain-like	8034385	3001732	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Tubulin C-terminal domain-like	8034385	3001732	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Tubulin nucleotide-binding domain-like	8034383	3001758	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tubulin C-terminal domain-like	8034387	3001732	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tubulin nucleotide-binding domain-like	8034386	3001758	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Tubulin C-terminal domain-like	8034387	3001732	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Tubulin nucleotide-binding domain-like	8034386	3001758	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Stathmin	8041515	3001374	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	TTL	e5xafF1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: TTL	ECOD (1.6)
A	Tubulin_C	e5xafA1	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	e5xafA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Tubulin nucleotide-binding domain-like	F: Tubulin	ECOD (1.6)
C	Tubulin_C	e5xafC1	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)
C	Tubulin	e5xafC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Tubulin nucleotide-binding domain-like	F: Tubulin	ECOD (1.6)
B	Tubulin_C	e5xafB2	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	e5xafB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Tubulin nucleotide-binding domain-like	F: Tubulin	ECOD (1.6)
D	Tubulin_C	e5xafD1	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)
D	Tubulin	e5xafD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Tubulin nucleotide-binding domain-like	F: Tubulin	ECOD (1.6)
E	Stathmin	e5xafE1	A: extended segments	X: Stathmin (From Topology)	H: Stathmin (From Topology)	T: Stathmin	F: Stathmin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.11480	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
F	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
F	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	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	3.40.50.1440	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Tubulin/FtsZ, GTPase domain	CATH (4.3.0)
C	3.30.1330.20	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
C	1.10.287.600	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
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)
D	3.40.50.1440	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Tubulin/FtsZ, GTPase domain	CATH (4.3.0)
D	3.30.1330.20	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
D	1.10.287.600	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix hairpin bin	CATH (4.3.0)
E	6.10.280.30	Special	Helix non-globular	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	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, C	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
B, D	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, D	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
F	TTL Protein	-	-	-
A, C	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
B, D	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
E	Stathmin-4	cytoskeletal protein binding protein binding binding tubulin binding	regulation of cytoskeleton organization regulation of microtubule polymerization or depolymerization regulation of biological process regulation of cellular component organization regulation of cellular process microtubule cytoskeleton organization biological regulation regulation of microtubule-based process regulation of organelle organization cellular component organization organelle organization microtubule polymerization or depolymerization cellular process microtubule-based process regulation of cytoskeleton organization regulation of microtubule polymerization or depolymerization regulation of biological process regulation of cellular component organization regulation of cellular process microtubule cytoskeleton organization biological regulation regulation of microtubule-based process regulation of organelle organization cellular component organization organelle organization microtubule polymerization or depolymerization cellular process microtubule-based process cellular component organization or biogenesis cytoskeleton organization regulation of microtubule cytoskeleton organization cellular component disassembly protein-containing complex organization protein-containing complex disassembly microtubule depolymerization supramolecular fiber organization protein depolymerization developmental process multicellular organismal process plasma membrane bounded cell projection organization cellular developmental process cell projection organization cell development neuron projection development nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation neuron development anatomical structure development system development	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system growth cone axon cell projection distal axon neuron projection membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system growth cone axon cell projection distal axon neuron projection plasma membrane bounded cell projection site of polarized growth

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR003008	Tubulin/FtsZ, GTPase domain	Domain
A, C	IPR008280	Tubulin/FtsZ, C-terminal	Homologous Superfamily
A, C	IPR037103	Tubulin/FtsZ-like, C-terminal domain	Homologous Superfamily
A, C	IPR017975	Tubulin, conserved site	Conserved Site
A, C	IPR002452	Alpha tubulin	Family
A, C	IPR000217	Tubulin	Family
A, C	IPR023123	Tubulin, C-terminal	Homologous Superfamily
A, C	IPR018316	Tubulin/FtsZ, 2-layer sandwich domain	Domain
A, C	IPR036525	Tubulin/FtsZ, GTPase domain superfamily	Homologous Superfamily
B, D	IPR003008	Tubulin/FtsZ, GTPase domain	Domain
B, D	IPR008280	Tubulin/FtsZ, C-terminal	Homologous Superfamily
B, D	IPR037103	Tubulin/FtsZ-like, C-terminal domain	Homologous Superfamily
B, D	IPR017975	Tubulin, conserved site	Conserved Site
B, D	IPR000217	Tubulin	Family
B, D	IPR023123	Tubulin, C-terminal	Homologous Superfamily
B, D	IPR002453	Beta tubulin	Family
B, D	IPR013838	Beta tubulin, autoregulation binding site	Binding Site
B, D	IPR018316	Tubulin/FtsZ, 2-layer sandwich domain	Domain
B, D	IPR036525	Tubulin/FtsZ, GTPase domain superfamily	Homologous Superfamily
E	IPR000956	Stathmin family	Family
E	IPR030514	Stathmin, conserved site	Conserved Site
E	IPR036002	Stathmin superfamily	Homologous Superfamily