3GVK | pdb_00003gvk

Crystal structure of endo-neuraminidase NF mutant

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)
A	d3gvka1	All beta proteins	6-bladed beta-propeller	Sialidases	Endo-alpha-sialidase	automated matches	Bacteriophage K1F (Escherichia phage K1F ) [TaxId: 344021 ],	SCOPe (2.08)
A	d3gvka2	All beta proteins	Triple-stranded beta-helix	Phage fibre proteins	automated matches	automated matches	Bacteriophage K1F (Escherichia phage K1F ) [TaxId: 344021 ],	SCOPe (2.08)
B	d3gvkb1	All beta proteins	6-bladed beta-propeller	Sialidases	Endo-alpha-sialidase	automated matches	Bacteriophage K1F (Escherichia phage K1F ) [TaxId: 344021 ],	SCOPe (2.08)
B	d3gvkb2	All beta proteins	Triple-stranded beta-helix	Phage fibre proteins	automated matches	automated matches	Bacteriophage K1F (Escherichia phage K1F ) [TaxId: 344021 ],	SCOPe (2.08)
B	d3gvkb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	Bacteriophage K1F (Escherichia phage K1F ) [TaxId: 344021 ],	SCOPe (2.08)
C	d3gvkc1	All beta proteins	6-bladed beta-propeller	Sialidases	Endo-alpha-sialidase	automated matches	Bacteriophage K1F (Escherichia phage K1F ) [TaxId: 344021 ],	SCOPe (2.08)
C	d3gvkc2	All beta proteins	Triple-stranded beta-helix	Phage fibre proteins	automated matches	automated matches	Bacteriophage K1F (Escherichia phage K1F ) [TaxId: 344021 ],	SCOPe (2.08)
C	d3gvkc3	Artifacts	Tags	Tags	Tags	N-terminal Tags	Bacteriophage K1F (Escherichia phage K1F ) [TaxId: 344021 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Phage fibre proteins	8042944	3000351	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Sialidases	8042942	3001607	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Bacteriophage endosialidase insert barrel domain-like	8052100	3002092	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Sialidases	8042942	3001607	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sialidases	8042942	3001607	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Bacteriophage endosialidase insert barrel domain-like	8052100	3002092	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phage fibre proteins	8042944	3000351	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sialidases	8042942	3001607	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Bacteriophage endosialidase N-terminal domain-like	8052101	3002093	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sialidases	8042942	3001607	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Bacteriophage endosialidase N-terminal domain-like	8052101	3002093	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Phage fibre proteins	8042944	3000351	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sialidases	8042942	3001607	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Bacteriophage endosialidase insert barrel domain-like	8052100	3002092	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	ABC_tran	e3gvkA1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: ABC_tran	ECOD (v294.1)
B	RVP	e3gvkB2	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
B	Cobalamin_bind	e3gvkB1	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Cobalamin_bind	ECOD (v294.1)
C	RVP	e3gvkC2	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
C	Cobalamin_bind	e3gvkC1	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Cobalamin_bind	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.750.60	Alpha Beta	2-Layer Sandwich	Transcription Regulator spoIIAA	Endosialidase, N-terminal extension domain	CATH (4.3.0)
A	2.120.10.10	Mainly Beta	6 Propeller	Neuraminidase		CATH (4.3.0)
A	2.40.30.20	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
A	4.10.1090.10	Few Secondary Structures	Irregular	Endosialidase, domain 4	Endosialidase, domain 4	CATH (4.3.0)
B	3.30.750.60	Alpha Beta	2-Layer Sandwich	Transcription Regulator spoIIAA	Endosialidase, N-terminal extension domain	CATH (4.3.0)
B	2.120.10.10	Mainly Beta	6 Propeller	Neuraminidase		CATH (4.3.0)
B	2.40.30.20	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B	4.10.1090.10	Few Secondary Structures	Irregular	Endosialidase, domain 4	Endosialidase, domain 4	CATH (4.3.0)
C	3.30.750.60	Alpha Beta	2-Layer Sandwich	Transcription Regulator spoIIAA	Endosialidase, N-terminal extension domain	CATH (4.3.0)
C	2.120.10.10	Mainly Beta	6 Propeller	Neuraminidase		CATH (4.3.0)
C	2.40.30.20	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
C	4.10.1090.10	Few Secondary Structures	Irregular	Endosialidase, domain 4	Endosialidase, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF12195	Beta barrel domain of bacteriophage endosialidase (End_beta_barrel)	Beta barrel domain of bacteriophage endosialidase	-	Repeat
A, B, C	PF12219	Catalytic domain of bacteriophage endosialidase (End_tail_spike)	Catalytic domain of bacteriophage endosialidase	-	Repeat
A, B, C	PF12218	N terminal extension of bacteriophage endosialidase (End_N_terminal)	N terminal extension of bacteriophage endosialidase	-	Repeat
A, B, C	PF12217	Catalytic beta propeller domain of bacteriophage endosialidase (End_beta_propel)	Catalytic beta propeller domain of bacteriophage endosialidase	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Endo-N-acetylneuraminidase	hydrolase activity, acting on glycosyl bonds endo-alpha-(2,8)-sialidase activity alpha-sialidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity identical protein binding protein binding binding	biological process involved in interspecies interaction between organisms symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction virion attachment to host cell adhesion of symbiont to host cell viral process viral life cycle adhesion of symbiont to host symbiont-mediated disruption of host anatomical structure symbiont-mediated disruption of host cell envelope symbiont-mediated disruption of host cellular anatomical structure symbiont entry into host cell via disruption of host cell envelope symbiont entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction virion attachment to host cell adhesion of symbiont to host cell viral process viral life cycle adhesion of symbiont to host symbiont-mediated disruption of host anatomical structure symbiont-mediated disruption of host cell envelope symbiont-mediated disruption of host cellular anatomical structure symbiont entry into host cell via disruption of host cell envelope symbiont entry into host cell disruption of anatomical structure in another organism receptor-mediated virion attachment to host cell adhesion receptor-mediated virion attachment to host cell symbiont entry into host cell via disruption of host cell glycocalyx	virus tail, fiber virus tail virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR024427	Endosialidase, beta-barrel domain	Domain
A, B, C	IPR024428	Endosialidase, beta-propeller domain	Domain
A, B, C	IPR036278	Sialidase superfamily	Homologous Superfamily
A, B, C	IPR023366	ATP synthase subunit alpha, N-terminal domain-like superfamily	Homologous Superfamily
A, B, C	IPR024430	Endosialidase, C-terminal domain	Domain
A, B, C	IPR024429	Endosialidase, N-terminal extension domain	Domain
A, B, C	IPR040775	Tail spike TSP1/Gp66, N-terminal domain	Domain
A, B, C	IPR044914	Endosialidase, C-terminal domain superfamily	Homologous Superfamily
A, B, C	IPR005604	Bacteriophage T7 tail fibre protein-like, N-terminal domain	Domain
A, B, C	IPR001724	Glycosyl hydrolase 58	Family
A, B, C	IPR030392	Intramolecular chaperone auto-processing domain	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.