5M34 | pdb_00005m34

Structure of cobinamide-bound BtuF mutant W66Y, the periplasmic vitamin B12 binding protein in E.coli

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)
B	d5m34b1	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	TroA-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d5m34b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d5m34a_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	TroA-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Helical backbone metal receptor	8044007	3001679	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Helical backbone metal receptor	8044007	3001679	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)
B	Glyco_hydro_106	e5m34B1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Glyco_hydro_106	ECOD (develop294)
A	Glyco_hydro_106	e5m34A1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Glyco_hydro_106	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)
A	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01497	Periplasmic binding protein (Peripla_BP_2)	Periplasmic binding protein	This is sensor domain found in bacterial periplasmic binding proteins, several of which are involved in iron and cobalamin transport [1,2,3]. Among its ligands are siderophores bacillibactin, enterobactin and iron(III)-hydroxamates (Matilla et. al., ...	This is sensor domain found in bacterial periplasmic binding proteins, several of which are involved in iron and cobalamin transport [1,2,3]. Among its ligands are siderophores bacillibactin, enterobactin and iron(III)-hydroxamates (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1 https://doi.org/10.1093/femsre/fuab043).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Vitamin B12-binding protein	vitamin binding binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding	localization nitrogen compound transport transport vitamin transport cobalamin transport establishment of localization	cellular anatomical structure membrane ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cobalamin transport complex transmembrane transporter complex periplasmic space outer membrane-bounded periplasmic space cellular anatomical structure membrane ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cobalamin transport complex transmembrane transporter complex periplasmic space outer membrane-bounded periplasmic space cell envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR054828	Vitamin B12-binding protein	Family
A, B	IPR023544	ABC transporter, vitamin B12-binding protein	Family
A, B	IPR002491	ABC transporter periplasmic binding domain	Domain
A, B	IPR050902	ABC Transporter Solute-Binding	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.