6W6E

The Mycobacterium tuberculosis ClpB disaggregase hexamer structure with a locally refined ClpB middle domain and a DnaK nucleotide binding domain

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF10431	e6w6eA3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF10431	ECOD (1.6)
A	PF17871	e6w6eA2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17871	ECOD (1.6)
A	PF00004	e6w6eA4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00004	ECOD (1.6)
A	PF07724	e6w6eA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF07724	ECOD (1.6)
E	PF10431	e6w6eE1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF10431	ECOD (1.6)
E	PF17871	e6w6eE2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17871	ECOD (1.6)
E	PF00004	e6w6eE4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00004	ECOD (1.6)
E	PF07724	e6w6eE3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF07724	ECOD (1.6)
B	PF10431	e6w6eB4	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF10431	ECOD (1.6)
B	PF17871	e6w6eB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17871	ECOD (1.6)
B	PF00004	e6w6eB3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00004	ECOD (1.6)
B	PF07724	e6w6eB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF07724	ECOD (1.6)
C	PF10431	e6w6eC2	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF10431	ECOD (1.6)
C	PF17871	e6w6eC3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17871	ECOD (1.6)
C	PF00004	e6w6eC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00004	ECOD (1.6)
C	PF07724	e6w6eC4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF07724	ECOD (1.6)
D	PF10431	e6w6eD3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF10431	ECOD (1.6)
D	PF17871	e6w6eD1	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17871	ECOD (1.6)
D	PF00004	e6w6eD2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00004	ECOD (1.6)
D	PF07724	e6w6eD4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF07724	ECOD (1.6)
F	PF10431	e6w6eF4	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF10431	ECOD (1.6)
F	PF17871	e6w6eF3	A: alpha arrays	X: Histone-like	H: Histone-related	T: AAA+ ATPase lid domain	F: PF17871	ECOD (1.6)
F	PF00004	e6w6eF1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00004	ECOD (1.6)
F	PF07724	e6w6eF2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF07724	ECOD (1.6)
G [auth I]	PF00012	e6w6eI2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00012	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF10431	C-terminal, D2-small domain, of ClpB protein (ClpB_D2-small)	C-terminal, D2-small domain, of ClpB protein	This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, Pfam:PF00004) it lacks the long coiled-coil insertion, and instead of helix C4 ...	This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, Pfam:PF00004) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit and thereby providing enough binding energy to stabilise the functional assembly [1]. The domain is associated with two Clp_N, Pfam:PF02861, at the N-terminus as well as AAA, Pfam:PF00004 and AAA_2, Pfam:PF07724.	Domain
A, B, C, D, E A, B, C, D, E, F	PF17871	AAA lid domain (AAA_lid_9)	AAA lid domain	This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.	Domain
A, B, C, D, E A, B, C, D, E, F	PF00004	ATPase family associated with various cellular activities (AAA) (AAA)	ATPase family associated with various cellular activities (AAA)	AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].	Domain
A, B, C, D, E A, B, C, D, E, F	PF07724	AAA domain (Cdc48 subfamily) (AAA_2)	AAA domain (Cdc48 subfamily)	This Pfam entry includes some of the AAA proteins not detected by the Pfam:PF00004 model.	Domain
G [auth I]	PF00012	Hsp70 protein (HSP70)	Hsp70 protein	-	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	Chaperone protein ClpB	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ATP hydrolysis 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 ATP-dependent activity	protein refolding organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein folding biosynthetic process organic substance biosynthetic process metabolic process cellular process protein refolding organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein folding biosynthetic process organic substance biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus	cell periphery plasma membrane membrane cellular anatomical entity external encapsulating structure cell wall peptidoglycan-based cell wall intracellular anatomical structure cytoplasm
G [auth I]	Chaperone protein DnaK	protein binding binding heat shock protein binding ATP-dependent protein folding chaperone protein folding chaperone ATP-dependent activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding protein binding binding heat shock protein binding ATP-dependent protein folding chaperone protein folding chaperone ATP-dependent activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding unfolded protein binding enzyme binding zymogen binding fibronectin binding pyrophosphatase activity ATP hydrolysis 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	protein refolding organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein folding biosynthetic process organic substance biosynthetic process metabolic process cellular process protein refolding organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein folding biosynthetic process organic substance biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process response to copper ion response to stimulus response to metal ion response to chemical response to inorganic substance cellular response to stimulus cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress response to superoxide cellular response to oxygen-containing compound response to reactive oxygen species cellular response to oxygen radical response to oxidative stress cellular response to reactive oxygen species cellular response to chemical stimulus cellular response to stress response to stress cellular response to superoxide response to oxygen radical regulation of protein maturation positive regulation of protein maturation regulation of cellular process positive regulation of macromolecule biosynthetic process positive regulation of protein processing regulation of primary metabolic process positive regulation of metabolic process positive regulation of plasminogen activation regulation of proteolysis proteolysis positive regulation of macromolecule metabolic process plasminogen activation zymogen activation regulation of biological process regulation of protein metabolic process regulation of cellular metabolic process regulation of gene expression positive regulation of proteolysis regulation of protein processing protein processing regulation of macromolecule biosynthetic process regulation of metabolic process positive regulation of protein metabolic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process regulation of plasminogen activation positive regulation of cellular process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process regulation of cellular biosynthetic process positive regulation of gene expression positive regulation of cellular biosynthetic process response to antibiotic regulation of molecular function positive regulation of molecular function regulation of DNA binding regulation of binding positive regulation of transcription regulatory region DNA binding regulation of transcription regulatory region DNA binding positive regulation of binding positive regulation of DNA binding protein phosphorylation protein autophosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein modification process phosphorus metabolic process chaperone cofactor-dependent protein refolding chaperone-mediated protein folding 'de novo' protein folding 'de novo' post-translational protein folding response to heat response to abiotic stimulus response to temperature stimulus	cell periphery external encapsulating structure glycocalyx cellular anatomical entity capsule membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle bacterial extracellular vesicle vesicle extracellular membrane-bounded organelle cell surface cell periphery external encapsulating structure glycocalyx cellular anatomical entity capsule membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle bacterial extracellular vesicle vesicle extracellular membrane-bounded organelle cell surface intracellular anatomical structure cytoplasm cytosol plasma membrane membrane cell wall peptidoglycan-based cell wall
H [auth N]	Substrate	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR001270	ClpA/B family	Family
A, B, C, D, E A, B, C, D, E, F	IPR018368	ClpA/B, conserved site 1	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR041546	ClpA/ClpB, AAA lid domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR004176	Clp, repeat (R) domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR028299	ClpA/B, conserved site 2	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR017730	Chaperonin ClpB	Family
A, B, C, D, E A, B, C, D, E, F	IPR003593	AAA+ ATPase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003959	ATPase, AAA-type, core	Domain
A, B, C, D, E A, B, C, D, E, F	IPR019489	Clp ATPase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036628	Clp, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
G [auth I]	IPR018181	Heat shock protein 70, conserved site	Conserved Site
G [auth I]	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
G [auth I]	IPR012725	Chaperone DnaK	Family
G [auth I]	IPR029048	Heat shock protein 70kD, C-terminal domain superfamily	Homologous Superfamily
G [auth I]	IPR029047	Heat shock protein 70kD, peptide-binding domain superfamily	Homologous Superfamily
G [auth I]	IPR013126	Heat shock protein 70 family	Family

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 R01GM133198.

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6W6E

The Mycobacterium tuberculosis ClpB disaggregase hexamer structure with a locally refined ClpB middle domain and a DnaK nucleotide binding domain

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage