4EMN | pdb_00004emn

Crystal structure of RpfB catalytic domain in complex with benzamidine

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)
D	d4emnd_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	RPF-like	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
C	d4emnc_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	RPF-like	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d4emnb_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	RPF-like	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d4emna_	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	RPF-like	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Lysozyme-like	8033417	3001879	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Lysozyme-like	8033417	3001879	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Lysozyme-like	8033417	3001879	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Lysozyme-like	8033417	3001879	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)
D	Transglycosylas	e4emnD1	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Transglycosylas	ECOD (1.6)
C	Transglycosylas	e4emnC1	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Transglycosylas	ECOD (1.6)
B	Transglycosylas	e4emnB1	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Transglycosylas	ECOD (1.6)
A	Transglycosylas	e4emnA1	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Transglycosylas	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)
C	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)
B	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)
A	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF06737	Transglycosylase-like domain (Transglycosylas)	Transglycosylase-like domain	This family of proteins are very likely to act as transglycosylase enzymes related to Pfam:PF00062 and Pfam:PF01464. These other families are weakly matched by this family, and include the known active site residues.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Probable resuscitation-promoting factor rpfB	hydrolase activity catalytic activity	regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process response to stimulus signaling quorum sensing cell-cell signaling detection of cell density detection of biotic stimulus response to biotic stimulus cell communication detection of stimulus cell population proliferation regulation of cell population proliferation developmental process biological process involved in interspecies interaction between organisms dormancy exit of symbiont in host formation of structure involved in a symbiotic process development of symbiont in host dormancy process negative regulation of metabolic process negative regulation of biological process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process negative regulation of macromolecule metabolic process	cellular anatomical structure extracellular region cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR010618	Resuscitation-promoting factor, core lysozyme-like domain	Domain
A, B, C, D	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR011098	G5 domain	Domain
A, B, C, D	IPR007137	Resuscitation-promoting factor, domain of unknown function DUF348	Domain
A, B, C, D	IPR051933	Bacterial Resuscitation-promoting factor RpfB	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.