6W6E | pdb_00006w6e

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
Domain Annotation: CATH
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)
G [auth I]		e6w6eI1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: P-II	F:	ECOD (20:10:01)
F		e6w6eF1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: SBP_bac_1	F:	ECOD (20:10:01)
E		e6w6eE1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: SBP_bac_1	F:	ECOD (20:10:01)
D		e6w6eD1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: SBP_bac_1	F:	ECOD (20:10:01)
C		e6w6eC1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: SBP_bac_1	F:	ECOD (20:10:01)
B		e6w6eB1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: SBP_bac_1	F:	ECOD (20:10:01)
A		e6w6eA1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: P-II	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G [auth I]	3.90.640.10	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (utative)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G [auth I]	PF00012	Hsp70 protein (HSP70)	Hsp70 protein	-	Family
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H [auth N]	Substrate	-	-	-
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 anion 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 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 primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein folding biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process response to copper ion response to stimulus response to metal ion protein refolding primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein folding 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 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 protein metabolic process positive regulation of biological 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 positive regulation of biosynthetic process proteolysis regulation of plasminogen activation positive regulation of macromolecule metabolic process plasminogen activation positive regulation of cellular process zymogen activation regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process regulation of gene expression positive regulation of gene expression positive regulation of proteolysis regulation of protein processing protein processing regulation of macromolecule biosynthetic process regulation of metabolic process response to antibiotic response to heat response to abiotic stimulus response to temperature stimulus	cell periphery cellular anatomical structure external encapsulating structure glycocalyx capsule membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle bacterial extracellular vesicle vesicle extracellular membrane-bounded organelle cell surface cell periphery cellular anatomical structure external encapsulating structure glycocalyx 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
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 anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide 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 primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein folding biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process cellular response to stimulus cellular response to heat response to stimulus protein refolding primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein folding 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 cellular anatomical structure plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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) N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR050130	ATP-dependent Clp protease/Chaperone ClpA/ClpB	Family
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

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.