7ZML

Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G1-001

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DEAD_1	e7zmlA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_1	ECOD (1.6)
A	Helicase_C_5	e7zmlA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_5	ECOD (1.6)
B	DEAD_1	e7zmlB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_1	ECOD (1.6)
B	Helicase_C_5	e7zmlB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_5	ECOD (1.6)
C	DEAD_1	e7zmlC2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_1	ECOD (1.6)
C	Helicase_C_5	e7zmlC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_5	ECOD (1.6)
D	DEAD_1	e7zmlD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD_1	ECOD (1.6)
D	Helicase_C_5	e7zmlD2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_5	ECOD (1.6)
E [auth K]	V-set_8	e7zmlK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
F [auth E]	V-set_8	e7zmlE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
G [auth F]	V-set_8	e7zmlF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
H [auth G]	V-set_8	e7zmlG1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E [auth K], F [auth E], G [auth F], H [auth G]	Heavy Chain	IGHV1	-	atp-dependent dna helicase q5	SAbDab (2024-11-08)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00270	DEAD/DEAH box helicase (DEAD)	DEAD/DEAH box helicase	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ...	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.	Domain
A, B, C, D	PF00271	Helicase conserved C-terminal domain (Helicase_C)	Helicase conserved C-terminal domain	The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.	Domain
A, B, C, D	PF16124	RecQ zinc-binding (RecQ_Zn_bind)	RecQ zinc-binding	This domain is the zinc-binding domain of ATP-dependent DNA helicase RecQ [1-2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	ATP-dependent DNA helicase Q5	catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA 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 DNA binding nucleic acid binding basal transcription machinery binding RNA polymerase binding protein binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding enzyme binding four-way junction helicase activity isomerase 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 3'-5' DNA helicase activity cation binding metal ion binding identical protein binding	cellular process cell cycle mitotic cell cycle nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus regulation of DNA recombination regulation of cellular process response to stimulus cellular process cell cycle mitotic cell cycle nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus regulation of DNA recombination regulation of cellular process response to stimulus regulation of double-strand break repair regulation of cellular response to stress negative regulation of biological process regulation of primary metabolic process negative regulation of DNA repair cellular response to stress response to stress regulation of response to stress negative regulation of double-strand break repair negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process recombinational repair regulation of nucleobase-containing compound metabolic process negative regulation of double-strand break repair via homologous recombination double-strand break repair via homologous recombination DNA repair negative regulation of macromolecule metabolic process double-strand break repair regulation of biological process negative regulation of response to stimulus negative regulation of metabolic process DNA recombination biological regulation regulation of macromolecule metabolic process regulation of DNA repair regulation of double-strand break repair via homologous recombination negative regulation of DNA recombination DNA damage response regulation of response to stimulus negative regulation of DNA metabolic process regulation of metabolic process regulation of DNA metabolic process replication-born double-strand break repair via sister chromatid exchange cellular response to nitrogen compound response to alcohol cellular response to organic cyclic compound response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound response to alkaloid cellular response to chemical stimulus cellular response to alcohol response to camptothecin cellular response to camptothecin response to chemical cellular response to alkaloid response to organic cyclic compound cell division negative regulation of transcription elongation by RNA polymerase II negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of DNA-templated transcription elongation negative regulation of DNA-templated transcription regulation of transcription elongation by RNA polymerase II cellular metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process negative regulation of DNA-templated transcription, elongation regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process transcription elongation by RNA polymerase II cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process DNA-templated transcription elongation negative regulation of biosynthetic process mitotic DNA replication DNA-templated DNA replication nuclear DNA replication cell cycle DNA replication mitotic cell cycle process mitotic DNA-templated DNA replication cell cycle process chromosome separation chromosome segregation cellular response to xenobiotic stimulus response to xenobiotic stimulus DNA duplex unwinding DNA geometric change chromosome organization DNA conformation change DNA unwinding involved in DNA replication cellular component organization organelle organization cellular component organization or biogenesis	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol transcription preinitiation complex protein-containing complex protein-DNA complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm intracellular anatomical structure cytoplasm cellular anatomical entity cytosol transcription preinitiation complex protein-containing complex protein-DNA complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular non-membrane-bounded organelle chromosome non-membrane-bounded organelle replication fork
E [auth K], F [auth E], G [auth F], H [auth G]	Gluebody G1-001	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR032284	ATP-dependent DNA helicase RecQ, zinc-binding domain	Domain
A, B, C, D	IPR002464	DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site	Conserved Site
A, B, C, D	IPR011545	DEAD/DEAH box helicase domain	Domain
A, B, C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D	IPR001650	Helicase, C-terminal domain-like	Domain
A, B, C, D	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B, C, D	IPR010716	RecQ helicase-like 5	Domain
A, B, C, D	IPR013257	Set2 Rpb1 interacting domain	Domain
A, B, C, D	IPR004589	DNA helicase, ATP-dependent, RecQ type	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: O94762	Bloom syndrome ovarian cancer spina bifida malignant mesothelioma pancreatic intraductal papillary-mucinous neoplasm Werner syndrome osteosarcoma Rothmund-Thomson syndrome

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.