5M2Q

Structure of cobinamide-bound BtuF mutant W66F, 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)
A	d5m2qa_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	TroA-like	automated matches	(Escherichia coli ) [TaxId: 562 ], (Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d5m2qb1	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	TroA-like	automated matches	(Escherichia coli ) [TaxId: 562 ], (Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d5m2qb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ], (Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Helical backbone metal receptor	8044007	3001679	SCOP2B (2022-06-29)
B	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)
A	Peripla_BP_2_N	e5m2qA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: Peripla_BP_2_N	ECOD (1.6)
B	Peripla_BP_2_N	e5m2qB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: Peripla_BP_2_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)
B	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	Outer membrane protein A,Vitamin B12-binding protein	wide pore channel activity passive transmembrane transporter activity channel activity porin activity transporter activity transmembrane transporter activity monoatomic ion transmembrane transporter activity identical protein binding protein binding binding vitamin binding cobalamin binding organic cyclic compound binding tetrapyrrole binding wide pore channel activity passive transmembrane transporter activity channel activity porin activity transporter activity transmembrane transporter activity monoatomic ion transmembrane transporter activity identical protein binding protein binding binding vitamin binding cobalamin binding organic cyclic compound binding tetrapyrrole binding heterocyclic compound binding small molecule binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process localization transport monoatomic ion transport establishment of localization biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process localization transport monoatomic ion transport establishment of localization biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction response to other organism detection of virus response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus nitrogen compound transport vitamin transport cobalamin transport	membrane cellular anatomical entity outer membrane protein-containing complex outer membrane protein complex membrane protein complex outer membrane-bounded periplasmic space cell envelope periplasmic space pore complex cell periphery cell outer membrane external encapsulating structure ATPase dependent transmembrane transport complex membrane cellular anatomical entity outer membrane protein-containing complex outer membrane protein complex membrane protein complex outer membrane-bounded periplasmic space cell envelope periplasmic space pore complex cell periphery cell outer membrane external encapsulating structure ATPase dependent transmembrane transport complex plasma membrane protein complex plasma membrane transporter complex ATP-binding cassette (ABC) transporter complex cobalamin transport complex transmembrane transporter complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR006664	Outer membrane protein, bacterial	Domain
A, B	IPR000498	Outer membrane protein OmpA-like, transmembrane domain	Domain
A, B	IPR006690	Outer membrane protein, OmpA-like, conserved site	Conserved Site
A, B	IPR050330	Bacterial Outer Membrane Structural/Functional	Family
A, B	IPR036737	OmpA-like domain superfamily	Homologous Superfamily
A, B	IPR011250	Outer membrane protein/outer membrane enzyme PagP, beta-barrel	Homologous Superfamily
A, B	IPR006665	OmpA-like domain	Domain
A, B	IPR002368	Outer membrane protein, OmpA	Family
A, B	IPR051030	Vitamin B12-binding component of ABC transporter	Family
A, B	IPR023544	ABC transporter, vitamin B12-binding protein	Family
A, B	IPR002491	ABC transporter periplasmic binding 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.