5OVW

Nanobody-bound BtuF, the vitamin B12 binding protein in Escherichia coli

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
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	d5ovwa_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	TroA-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d5ovwb_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	TroA-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d5ovwc_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	TroA-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d5ovwd_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	TroA-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d5ovwe_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	TroA-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d5ovwf_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	TroA-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d5ovwg1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
G	d5ovwg2	Artifacts	Tags	Tags	Tags	C-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
H	d5ovwh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
H	d5ovwh2	Artifacts	Tags	Tags	Tags	C-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
I	d5ovwi1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
I	d5ovwi2	Artifacts	Tags	Tags	Tags	C-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
J	d5ovwj1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
J	d5ovwj2	Artifacts	Tags	Tags	Tags	C-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
K	d5ovwk1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
K	d5ovwk2	Artifacts	Tags	Tags	Tags	C-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
L	d5ovwl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
L	d5ovwl2	Artifacts	Tags	Tags	Tags	C-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	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)
C	SCOP2B Superfamily	Helical backbone metal receptor	8044007	3001679	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Helical backbone metal receptor	8044007	3001679	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Helical backbone metal receptor	8044007	3001679	SCOP2B (2022-06-29)
F	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	e5ovwA2	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	e5ovwB1	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)
C	Peripla_BP_2_N	e5ovwC1	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)
D	Peripla_BP_2_N	e5ovwD1	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)
E	Peripla_BP_2_N	e5ovwE2	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)
F	Peripla_BP_2_N	e5ovwF2	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)
G	V-set_8	e5ovwG1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
H	V-set_8	e5ovwH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
I	V-set_8	e5ovwI1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
J	V-set_8	e5ovwJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
K	V-set_8	e5ovwK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
L	V-set_8	e5ovwL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	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)
C	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)
D	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)
E	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)
F	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
G, H, I, J, K G, H, I, J, K, L	Heavy Chain	IGHV1	-	vitamin b12-binding protein	SAbDab (2024-11-15)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	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, C, D, E A, B, C, D, E, F	Vitamin B12-binding protein	vitamin binding binding cobalamin binding organic cyclic compound 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
G, H, I, J, K G, H, I, J, K, L	Nanobody	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR051030	Vitamin B12-binding component of ABC transporter	Family
A, B, C, D, E A, B, C, D, E, F	IPR023544	ABC transporter, vitamin B12-binding protein	Family
A, B, C, D, E A, B, C, D, E, F	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.