5YQR | pdb_00005yqr

Crystal structure of the PH-like domain of Lam6

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
Membrane Protein Annotation: OPM

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Lysozyme-like	8033861	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)
A	Chromo	e5yqrA1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Chromo	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.530.40	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00959	Phage lysozyme (Phage_lysozyme)	Phage lysozyme	This family includes lambda phage lysozyme and E. coli endolysin.	Domain
A	PF02893	GRAM domain (GRAM)	GRAM domain	The GRAM domain is found in in glucosyltransferases, myotubularins and other putative membrane-associated proteins. Note the alignment is lacking the last two beta strands and alpha helix.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Endolysin/Membrane-anchored lipid-binding protein LAM6 fusion protein	hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity sterol binding binding steroid binding lipid binding sterol transfer activity lipid transporter activity lipid transfer activity transporter activity	defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process aminoglycan metabolic process peptidoglycan metabolic process metabolic process cellular process macromolecule metabolic process symbiont-mediated cytolysis of host cell viral life cycle disruption of cell in another organism cytolysis biological process involved in interaction with host biological process involved in symbiotic interaction viral release from host cell by cytolysis exit from host cell viral process cytolysis in another organism viral release from host cell disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing cell wall organization or biogenesis cell wall macromolecule catabolic process cell wall macromolecule metabolic process cellular localization transport intracellular lipid transport lipid localization lipid transport intracellular transport organic hydroxy compound transport intracellular sterol transport establishment of localization localization macromolecule localization establishment of localization in cell sterol transport	host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle organelle membrane contact site mitochondria-associated endoplasmic reticulum membrane contact site vacuole-mitochondrion membrane contact site nucleus-vacuole junction cell cortex cortical endoplasmic reticulum organelle subcompartment endomembrane system cell periphery endoplasmic reticulum subcompartment endoplasmic reticulum endoplasmic reticulum tubular network plasma membrane membrane endoplasmic reticulum-plasma membrane contact site nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR052619	Bacteriophage lysozyme-like	Family
A	IPR001165	T4-type lysozyme	Family
A	IPR034690	Endolysin T4 type	Family
A	IPR002196	Glycoside hydrolase, family 24	Family
A	IPR023347	Lysozyme domain superfamily	Homologous Superfamily
A	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily
A	IPR011993	PH-like domain superfamily	Homologous Superfamily
A	IPR031968	VASt domain	Domain
A	IPR051482	Cholesterol transport domain-containing protein	Family
A	IPR004182	GRAM domain	Domain

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	OPM	Monotopic/peripheral	All beta monotopic/peripheral	PH domain-like	Pleckstrin-homology domain

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.