3DPQ

Crystal structure of the substrate binding domain of E. coli DnaK in complex with a long pyrrhocoricin-derived inhibitor peptide (form B)

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	Heat shock protein 70kD (HSP70) C-terminal subdomain	8035544	3000668	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	heat shock protein 70kd (hsp70) peptide-binding domain	8035545	3000642	SCOP2B (2022-06-29)
D [auth F]	SCOP2B Superfamily	heat shock protein 70kd (hsp70) peptide-binding domain	8035545	3000642	SCOP2B (2022-06-29)
D [auth F]	SCOP2B Superfamily	Heat shock protein 70kD (HSP70) C-terminal subdomain	8035544	3000668	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	heat shock protein 70kd (hsp70) peptide-binding domain	8035545	3000642	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Heat shock protein 70kD (HSP70) C-terminal subdomain	8035544	3000668	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	Heat shock protein 70kD (HSP70) C-terminal subdomain	8035544	3000668	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	heat shock protein 70kd (hsp70) peptide-binding domain	8035545	3000642	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	HSP70_2nd	e3dpqB1	A: beta sandwiches	X: Heat shock protein 70kD (HSP70), peptide-binding domain (From Topology)	H: Heat shock protein 70kD (HSP70), peptide-binding domain (From Topology)	T: Heat shock protein 70kD (HSP70), peptide-binding domain	F: HSP70_2nd	ECOD (1.6)
B	HSP70_3rd	e3dpqB2	A: alpha bundles	X: immunoglobulin/albumin-binding domain-like	H: Heat shock protein 70kD (HSP70), C-terminal subdomain (From Topology)	T: Heat shock protein 70kD (HSP70), C-terminal subdomain	F: HSP70_3rd	ECOD (1.6)
D [auth F]	HSP70_2nd	e3dpqF1	A: beta sandwiches	X: Heat shock protein 70kD (HSP70), peptide-binding domain (From Topology)	H: Heat shock protein 70kD (HSP70), peptide-binding domain (From Topology)	T: Heat shock protein 70kD (HSP70), peptide-binding domain	F: HSP70_2nd	ECOD (1.6)
D [auth F]	HSP70_3rd	e3dpqF2	A: alpha bundles	X: immunoglobulin/albumin-binding domain-like	H: Heat shock protein 70kD (HSP70), C-terminal subdomain (From Topology)	T: Heat shock protein 70kD (HSP70), C-terminal subdomain	F: HSP70_3rd	ECOD (1.6)
A	HSP70_2nd	e3dpqA1	A: beta sandwiches	X: Heat shock protein 70kD (HSP70), peptide-binding domain (From Topology)	H: Heat shock protein 70kD (HSP70), peptide-binding domain (From Topology)	T: Heat shock protein 70kD (HSP70), peptide-binding domain	F: HSP70_2nd	ECOD (1.6)
A	HSP70_3rd	e3dpqA2	A: alpha bundles	X: immunoglobulin/albumin-binding domain-like	H: Heat shock protein 70kD (HSP70), C-terminal subdomain (From Topology)	T: Heat shock protein 70kD (HSP70), C-terminal subdomain	F: HSP70_3rd	ECOD (1.6)
C [auth E]	HSP70_2nd	e3dpqE1	A: beta sandwiches	X: Heat shock protein 70kD (HSP70), peptide-binding domain (From Topology)	H: Heat shock protein 70kD (HSP70), peptide-binding domain (From Topology)	T: Heat shock protein 70kD (HSP70), peptide-binding domain	F: HSP70_2nd	ECOD (1.6)
C [auth E]	HSP70_3rd	e3dpqE2	A: alpha bundles	X: immunoglobulin/albumin-binding domain-like	H: Heat shock protein 70kD (HSP70), C-terminal subdomain (From Topology)	T: Heat shock protein 70kD (HSP70), C-terminal subdomain	F: HSP70_3rd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.34.10	Mainly Beta	Sandwich	Substrate Binding Domain Of DNAk	Chain A, domain 1	CATH (4.3.0)
B	1.20.1270.10	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
D [auth F]	2.60.34.10	Mainly Beta	Sandwich	Substrate Binding Domain Of DNAk	Chain A, domain 1	CATH (4.3.0)
D [auth F]	1.20.1270.10	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
A	2.60.34.10	Mainly Beta	Sandwich	Substrate Binding Domain Of DNAk	Chain A, domain 1	CATH (4.3.0)
A	1.20.1270.10	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)
C [auth E]	2.60.34.10	Mainly Beta	Sandwich	Substrate Binding Domain Of DNAk	Chain A, domain 1	CATH (4.3.0)
C [auth E]	1.20.1270.10	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C [auth E], D [auth F]	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 [auth E], D [auth F]	Chaperone protein 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 organic cyclic compound 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 protein-macromolecule adaptor activity molecular adaptor 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 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 nucleobase-containing compound metabolic process organic cyclic 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 chaperone cofactor-dependent protein refolding chaperone-mediated protein folding 'de novo' protein folding 'de novo' post-translational protein folding cellular response to stimulus response to organic substance cellular response to topologically incorrect protein response to stimulus cellular response to unfolded protein response to unfolded protein cellular response to chemical stimulus cellular response to stress response to chemical response to stress response to topologically incorrect protein cellular response to organic substance response to heat response to abiotic stimulus response to temperature stimulus response to copper ion response to metal ion stress response to copper ion stress response to metal ion response to inorganic substance	membrane cellular anatomical entity intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane inclusion body protein-containing complex
E [auth C], F [auth D], G, H	inhibitor peptide	-	biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus defense response to bacterium response to bacterium	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C [auth E], D [auth F]	IPR018181	Heat shock protein 70, conserved site	Conserved Site
A, B, C [auth E], D [auth F]	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
A, B, C [auth E], D [auth F]	IPR012725	Chaperone DnaK	Family
A, B, C [auth E], D [auth F]	IPR029048	Heat shock protein 70kD, C-terminal domain superfamily	Homologous Superfamily
A, B, C [auth E], D [auth F]	IPR029047	Heat shock protein 70kD, peptide-binding domain superfamily	Homologous Superfamily
A, B, C [auth E], D [auth F]	IPR013126	Heat shock protein 70 family	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.