1DKG | pdb_00001dkg

CRYSTAL STRUCTURE OF THE NUCLEOTIDE EXCHANGE FACTOR GRPE BOUND TO THE ATPASE DOMAIN OF THE MOLECULAR CHAPERONE DNAK

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)
C [auth D]	d1dkgd1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Actin/HSP70	Heat shock protein 70kDa, ATPase fragment	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1dkgb1	All beta proteins	Head domain of nucleotide exchange factor GrpE	Head domain of nucleotide exchange factor GrpE	Head domain of nucleotide exchange factor GrpE	Head domain of nucleotide exchange factor GrpE	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1dkgb2	Coiled coil proteins	Parallel coiled-coil	Coiled-coil domain of nucleotide exchange factor GrpE	Coiled-coil domain of nucleotide exchange factor GrpE	Coiled-coil domain of nucleotide exchange factor GrpE	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1dkga1	All beta proteins	Head domain of nucleotide exchange factor GrpE	Head domain of nucleotide exchange factor GrpE	Head domain of nucleotide exchange factor GrpE	Head domain of nucleotide exchange factor GrpE	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1dkga2	Coiled coil proteins	Parallel coiled-coil	Coiled-coil domain of nucleotide exchange factor GrpE	Coiled-coil domain of nucleotide exchange factor GrpE	Coiled-coil domain of nucleotide exchange factor GrpE	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth D]	SCOP2 Family	Actin/HSP70	8032097	4000313	SCOP2 (2022-06-29)
C [auth D]	SCOP2 Superfamily	Actin-like ATPases	8044476	3000092	SCOP2 (2022-06-29)
C [auth D]	SCOP2 Superfamily	Actin-like ATPases	8044475	3000092	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Head domain of nucleotide exchange factor GrpE	8042915	3001657	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Coiled-coil domain of nucleotide exchange factor GrpE	8039541	3001480	SCOP2B (2022-06-29)
A	SCOP2 Family	Coiled-coil domain of nucleotide exchange factor GrpE	8027162	4003783	SCOP2 (2022-06-29)
A	SCOP2 Family	Head domain of nucleotide exchange factor GrpE	8030536	4002724	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Coiled-coil domain of nucleotide exchange factor GrpE	8039541	3001480	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Head domain of nucleotide exchange factor GrpE	8042915	3001657	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth D]	Hexokinase_2	e1dkgD1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Hexokinase_2	ECOD (v294.1)
B	Acyl-CoA_dh_M	e1dkgB1	A: a/b three-layered sandwiches	X: HTH	H: PABC(PABP) domain	T: PABC(PABP) domain	F: Acyl-CoA_dh_M	ECOD (v294.1)
A	GrpE	e1dkgA1	A: beta complex topology	X: Head domain of nucleotide exchange factor GrpE	H: Head domain of nucleotide exchange factor GrpE	T: Head domain of nucleotide exchange factor GrpE	F: GrpE	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth D]	3.30.420.40	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C [auth D]	3.30.30.30	Alpha Beta	2-Layer Sandwich	Defensin A-like		CATH (4.3.0)
C [auth D]	3.90.640.10	Alpha Beta	Alpha-Beta Complex	Actin	Chain A, domain 4	CATH (4.3.0)
B	3.90.20.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
B	2.30.22.10	Mainly Beta	Roll	Nucleotide Exchange Factor Grpe	Chain A, domain 2	CATH (4.3.0)
A	3.90.20.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
A	2.30.22.10	Mainly Beta	Roll	Nucleotide Exchange Factor Grpe	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D]	MOLECULAR CHAPERONE DNAK	protein binding binding heat shock protein binding ATP-dependent protein folding chaperone protein folding chaperone ATP-dependent activity protein-folding chaperone binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding protein binding binding heat shock protein binding ATP-dependent protein folding chaperone protein folding chaperone ATP-dependent activity protein-folding chaperone 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 ADP binding unfolded protein binding sigma factor antagonist activity transcription corepressor activity transcription regulator activity transcription coregulator activity 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 cation binding transition metal ion binding zinc ion binding metal ion binding	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 nucleobase-containing compound metabolic process DNA replication DNA metabolic process 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 nucleobase-containing compound metabolic process DNA replication DNA metabolic process nucleic acid metabolic process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis protein unfolding cellular response to stimulus cellular response to topologically incorrect protein cellular response to stress response to stimulus response to stress response to topologically incorrect protein cellular response to unfolded protein response to unfolded protein response to heat response to abiotic stimulus response to temperature stimulus response to copper ion response to metal ion response to chemical stress response to copper ion stress response to metal ion	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane inclusion body protein-containing complex
A, B	NUCLEOTIDE EXCHANGE FACTOR GRPE	protein binding binding protein domain specific binding unfolded protein binding identical protein binding protein homodimerization activity protein dimerization activity enzyme regulator activity nucleoside-triphosphatase regulator activity molecular function regulator activity adenyl-nucleotide exchange factor activity ATPase regulator activity protein-folding chaperone binding	cellular process protein unfolding cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis protein folding biosynthetic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process cellular process protein unfolding cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis protein folding biosynthetic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation response to stimulus response to stress response to heat response to abiotic stimulus response to temperature stimulus	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth D]	IPR018181	Heat shock protein 70, conserved site	Conserved Site
C [auth D]	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
C [auth D]	IPR012725	Chaperone DnaK	Family
C [auth D]	IPR029048	Heat shock protein 70kD, C-terminal domain superfamily	Homologous Superfamily
C [auth D]	IPR029047	Heat shock protein 70kD, peptide-binding domain superfamily	Homologous Superfamily
C [auth D]	IPR013126	Heat shock protein 70 family	Family
A, B	IPR009012	GrpE nucleotide exchange factor, head	Homologous Superfamily
A, B	IPR013805	GrpE nucleotide exchange factor, coiled-coil	Homologous Superfamily
A, B	IPR000740	GrpE nucleotide exchange factor	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.