3SC3 | pdb_00003sc3

Crystal structure of a Putative DNA replication regulator Hda (Sama_1916) from SHEWANELLA AMAZONENSIS SB2B at 3.00 A resolution

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)
B	TPR_2, TPR_P4H	e3sc3B1	A: alpha bundles	X: Ribonuclease H-like	H: ARM repeat	T: ARM repeat	F: TPR_2, TPR_P4H	ECOD (develop294)
A	TPR_2, TPR_P4H	e3sc3A1	A: alpha bundles	X: Ribonuclease H-like	H: ARM repeat	T: ARM repeat	F: TPR_2, TPR_P4H	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF22688	Hda, lid domain (Hda_lid)	Hda, lid domain	This entry represents the C-terminal lid domain of the Regulatory inactivation of DnaA Hda protein from Shewanella amazonensis, the essential component of RIDA (regulatory inactivation of DnaA). This domain is a short four-helix bundle that contains ...	This entry represents the C-terminal lid domain of the Regulatory inactivation of DnaA Hda protein from Shewanella amazonensis, the essential component of RIDA (regulatory inactivation of DnaA). This domain is a short four-helix bundle that contains the sensor II motif [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Putative DNA replication regulator Hda	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of DNA-templated DNA replication initiation regulation of cellular process negative regulation of biological process negative regulation of DNA-templated DNA replication initiation nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of DNA-templated DNA replication initiation regulation of cellular process negative regulation of biological process negative regulation of DNA-templated DNA replication initiation regulation of primary metabolic process negative regulation of DNA-templated DNA replication negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of biological process negative regulation of DNA replication negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process regulation of DNA-templated DNA replication negative regulation of DNA metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR017788	DnaA regulatory inactivator Hda	Family
A, B	IPR020591	Chromosomal replication control, initiator DnaA-like	Family
A, B	IPR055199	Hda, lid domain	Domain
A, B	IPR013317	Chromosomal replication initiator protein DnaA, ATPAse domain	Domain
A, B	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.