6MW7 | pdb_00006mw7

Crystal structure of ATPase module of SMCHD1 bound to ATP

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
D	NAGidase	e6mw7D1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: Sodium/proton antiporter subunits-like	T: NADH-quinone oxidoreductase subunit 8 (Nqo8)-related	F: NAGidase	ECOD (develop294)
C	NAGidase	e6mw7C1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: Sodium/proton antiporter subunits-like	T: NADH-quinone oxidoreductase subunit 8 (Nqo8)-related	F: NAGidase	ECOD (develop294)
B	NAGidase	e6mw7B1	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: Sodium/proton antiporter subunits-like	T: NADH-quinone oxidoreductase subunit 8 (Nqo8)-related	F: NAGidase	ECOD (develop294)
A	HATPase_c_3	e6mw7A2	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: HATPase_c_3	ECOD (develop294)
A		e6mw7A3	A: alpha bundles	X: Family A G protein-coupled receptor-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F:	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF13589	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase (HATPase_c_3)	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase	This family represents, additionally, the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.	Domain
A, B, C, D	PF22899	SMCHD1, ribosomal S5 domain 2-like domain (SMCHD1_S5)	SMCHD1, ribosomal S5 domain 2-like domain	This domain is found in the homologues of human SMCHD1 protein. SMCHD1 is an epigenetic repressor that may participate in structural manipulation of chromatin in an ATP-dependent manner as a part of its role in gene expression regulation. This domain ...	This domain is found in the homologues of human SMCHD1 protein. SMCHD1 is an epigenetic repressor that may participate in structural manipulation of chromatin in an ATP-dependent manner as a part of its role in gene expression regulation. This domain follows the SMCHD1 ATPase module and adopts a globular alpha/beta structure consisting of five-stranded mixed beta-sheet with alpha helices packed on both sides. This domain is involved in dimerisation.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Structural maintenance of chromosomes flexible hinge domain-containing protein 1	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 DNA binding nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization 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 ATP-dependent activity	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 nucleobase-containing compound metabolic process cellular response to stress response to stress regulation of response to stress negative regulation of double-strand break repair negative regulation of cellular 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 nucleobase-containing compound metabolic process 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 primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid 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 metabolic process cellular process negative regulation of DNA metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process positive regulation of biological process positive regulation of response to stimulus positive regulation of metabolic process positive regulation of DNA repair positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of double-strand break repair via nonhomologous end joining positive regulation of double-strand break repair via nonhomologous end joining double-strand break repair via nonhomologous end joining positive regulation of double-strand break repair positive regulation of DNA metabolic process cellular component organization organelle organization chromosome organization cellular component organization or biogenesis developmental process multicellular organism development multicellular organismal process sensory organ development anatomical structure development animal organ development respiratory system development nose development system development sexual reproduction cellular developmental process reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation cell differentiation chromatin organization chromatin remodeling regulation of biosynthetic process epigenetic programming of gene expression epigenetic regulation of gene expression multicellular organismal reproductive process gene expression genomic imprinting macromolecule biosynthetic process regulation of gene expression autosome genomic imprinting biosynthetic process germ cell development regulation of macromolecule biosynthetic process cellular component biogenesis cellular component assembly heterochromatin formation sex-chromosome dosage compensation heterochromatin organization negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process dosage compensation by inactivation of X chromosome negative regulation of gene expression, epigenetic random inactivation of X chromosome	membrane-bounded organelle intracellular anatomical structure sex chromosome nucleus membrane-enclosed lumen intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen Barr body membrane-bounded organelle intracellular anatomical structure sex chromosome nucleus membrane-enclosed lumen intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen Barr body organelle membraneless organelle nuclear lumen X chromosome nucleoplasm site of double-strand break site of DNA damage nuclear body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
A, B, C, D	IPR038892	SMCHD1	Family
A, B, C, D	IPR010935	SMCs flexible hinge	Domain
A, B, C, D	IPR036277	SMCs flexible hinge superfamily	Homologous Superfamily
A, B, C, D	IPR058614	SMCHD1, Ig-like domain 5	Domain
A, B, C, D	IPR058611	SMCHD1, Ig-like domain 1	Domain
A, B, C, D	IPR058616	SMCHD1, Ig-like domain 8	Domain
A, B, C, D	IPR058615	SMCHD1, Ig-like domain 6	Domain
A, B, C, D	IPR055109	SMCHD1, ribosomal S5 domain 2-like domain	Domain
A, B, C, D	IPR058613	SMCHD1, Ig-like domain 4	Domain
A, B, C, D	IPR058612	SMCHD1, Ig-like domain 2	Domain
A, B, C, D	IPR058617	SMCHD1, Ig-like domain 7	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: A6NHR9	facioscapulohumeral muscular dystrophy 2 arhinia, choanal atresia, and microphthalmia myopathy facioscapulohumeral muscular dystrophy malignant ependymoma malignant pancreatic neoplasm multiple sclerosis muscular dystrophy osteosarcoma atypical teratoid rhabdoid tumor Pick disease cutaneous lupus erythematosus primitive neuroectodermal tumor rheumatoid arthritis glioblastoma facioscapulohumeral muscular dystrophy 2 arhinia, choanal atresia, and microphthalmia myopathy facioscapulohumeral muscular dystrophy malignant ependymoma malignant pancreatic neoplasm multiple sclerosis muscular dystrophy osteosarcoma atypical teratoid rhabdoid tumor Pick disease cutaneous lupus erythematosus primitive neuroectodermal tumor rheumatoid arthritis glioblastoma invasive ductal breast carcinoma large cell medulloblastoma malignant glioma medulloblastoma muscle tissue disease Muscular Dystrophy, Facioscapulohumeral arthrogryposis ovarian cancer congenital muscular dystrophy pituitary cancer exocrine pancreatic carcinoma progressive supranuclear palsy gastric cancer Sjogren syndrome IgA glomerulonephritis Kallmann syndrome limb-girdle muscular dystrophy malignant mesothelioma microphthalmia muscular disease astrocytic tumor pancreatic intraductal papillary-mucinous neoplasm conotruncal heart malformations psoriasis gastric carcinoma intellectual disability Klinefelter 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.