1VKD | pdb_00001vkd

Crystal structure of a predicted glycosidase (tm1225) from thermotoga maritima msb8 at 2.10 A resolution

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)
F	d1vkdf_	All beta proteins	5-bladed beta-propeller	Arabinanase/levansucrase/invertase	TM1225-like predicted glycosylases	Hypothetical protein TM1225	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
E	d1vkde_	All beta proteins	5-bladed beta-propeller	Arabinanase/levansucrase/invertase	TM1225-like predicted glycosylases	Hypothetical protein TM1225	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
D	d1vkdd_	All beta proteins	5-bladed beta-propeller	Arabinanase/levansucrase/invertase	TM1225-like predicted glycosylases	Hypothetical protein TM1225	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
C	d1vkdc_	All beta proteins	5-bladed beta-propeller	Arabinanase/levansucrase/invertase	TM1225-like predicted glycosylases	Hypothetical protein TM1225	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
B	d1vkdb_	All beta proteins	5-bladed beta-propeller	Arabinanase/levansucrase/invertase	TM1225-like predicted glycosylases	Hypothetical protein TM1225	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
A	d1vkda1	All beta proteins	5-bladed beta-propeller	Arabinanase/levansucrase/invertase	TM1225-like predicted glycosylases	Hypothetical protein TM1225	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
A	d1vkda2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Furanosidase-like	8041371	3000845	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Furanosidase-like	8041371	3000845	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Furanosidase-like	8041371	3000845	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Furanosidase-like	8041371	3000845	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Furanosidase-like	8041371	3000845	SCOP2B (2022-06-29)
A	SCOP2 Family	TM1225-like predicted glycosylases	8028992	4001864	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Furanosidase-like	8041371	3000845	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Ldl_recept_b	e1vkdF1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Ldl_recept_b	ECOD (v294.1)
E	Ldl_recept_b	e1vkdE1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Ldl_recept_b	ECOD (v294.1)
D	Ldl_recept_b	e1vkdD1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Ldl_recept_b	ECOD (v294.1)
C	Ldl_recept_b	e1vkdC1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Ldl_recept_b	ECOD (v294.1)
B	Ldl_recept_b	e1vkdB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Ldl_recept_b	ECOD (v294.1)
A	Glyco_hydro_130	e1vkdA1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 5-bladed	F: Glyco_hydro_130	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	2.115.10.20	Mainly Beta	5 Propeller	Tachylectin-2	Chain A	CATH (4.3.0)
E	2.115.10.20	Mainly Beta	5 Propeller	Tachylectin-2	Chain A	CATH (4.3.0)
D	2.115.10.20	Mainly Beta	5 Propeller	Tachylectin-2	Chain A	CATH (4.3.0)
C	2.115.10.20	Mainly Beta	5 Propeller	Tachylectin-2	Chain A	CATH (4.3.0)
B	2.115.10.20	Mainly Beta	5 Propeller	Tachylectin-2	Chain A	CATH (4.3.0)
A	2.115.10.20	Mainly Beta	5 Propeller	Tachylectin-2	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF04041	beta-1,4-mannooligosaccharide phosphorylase (Glyco_hydro_130)	beta-1,4-mannooligosaccharide phosphorylase	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	conserved hypothetical protein TM1225	glycosyltransferase activity transferase activity catalytic activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR007184	Mannoside phosphorylase	Family
A, B, C, D, E A, B, C, D, E, F	IPR023296	Glycosyl hydrolase, five-bladed beta-propeller domain superfamily	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.