4DBL | pdb_00004dbl

Crystal structure of E159Q mutant of BtuCDF

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J	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)
H	SCOP2B Superfamily	ABC transporter-like P-loop ATPases	8058248	3002020	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	ABC transporter-like P-loop ATPases	8058248	3002020	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ABC transporter-like P-loop ATPases	8058248	3002020	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ABC transporter-like P-loop ATPases	8058248	3002020	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	BtuC-like	8018502	3000523	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	BtuC-like	8018502	3000523	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	BtuC-like	8018502	3000523	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	BtuC-like	8018502	3000523	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)
J	Peripla_BP_2	e4dblJ1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Peripla_BP_2	ECOD (develop294)
E	Peripla_BP_2	e4dblE1	A: alpha bundles	X: Spectrin repeat-like	H: TIM barrels	T: TIM barrels	F: Peripla_BP_2	ECOD (develop294)
H	ABC_tran	e4dblH1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
I	ABC_tran	e4dblI1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
D	ABC_tran	e4dblD1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
C	SAM_1	e4dblC1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: SAM_1	ECOD (develop294)
G	ABC_tran	e4dblG1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
F	ABC_tran	e4dblF1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
B	ABC_tran	e4dblB1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
A	SAM_1	e4dblA1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: SAM_1	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J	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)
H	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
I	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
G	1.10.3470.10	Mainly Alpha	Orthogonal Bundle	ABC transporter involved in vitamin B12 uptake, BtuC	ABC transporter involved in vitamin B12 uptake, BtuC	CATH (4.3.0)
F	1.10.3470.10	Mainly Alpha	Orthogonal Bundle	ABC transporter involved in vitamin B12 uptake, BtuC	ABC transporter involved in vitamin B12 uptake, BtuC	CATH (4.3.0)
B	1.10.3470.10	Mainly Alpha	Orthogonal Bundle	ABC transporter involved in vitamin B12 uptake, BtuC	ABC transporter involved in vitamin B12 uptake, BtuC	CATH (4.3.0)
A	1.10.3470.10	Mainly Alpha	Orthogonal Bundle	ABC transporter involved in vitamin B12 uptake, BtuC	ABC transporter involved in vitamin B12 uptake, BtuC	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, J	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
C, D, H, I	PF00005	ABC transporter (ABC_tran)	ABC transporter	ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are comp ...	ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain Pfam:PF00664. These four domains may belong to a single polypeptide as in Swiss:P13569, or belong in different polypeptide chains.	Domain
A, B, F, G	PF01032	FecCD transport family (FecCD)	FecCD transport family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, J	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
C, D, H, I	Vitamin B12 import ATP-binding protein BtuD	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding active transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity transporter activity transmembrane transporter activity ATP-dependent activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ABC-type vitamin B12 transporter activity ABC-type transporter activity vitamin transmembrane transporter activity	localization nitrogen compound transport transport vitamin transport cobalamin transport establishment of localization	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex BtuCD complex cobalamin transport complex extrinsic component of membrane
A, B, F, G	Vitamin B12 import system permease protein BtuC	ABC-type vitamin B12 transporter activity ABC-type transporter activity active transmembrane transporter activity vitamin transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity transporter activity transmembrane transporter activity ATP-dependent activity identical protein binding protein binding binding	localization nitrogen compound transport transport vitamin transport cobalamin transport establishment of localization	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex BtuCD complex cobalamin transport complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, J	IPR054828	Vitamin B12-binding protein	Family
E, J	IPR023544	ABC transporter, vitamin B12-binding protein	Family
E, J	IPR002491	ABC transporter periplasmic binding domain	Domain
E, J	IPR050902	ABC Transporter Solute-Binding	Family
C, D, H, I	IPR017871	ABC transporter-like, conserved site	Conserved Site
C, D, H, I	IPR050153	Metal Ion Import ATP-binding	Family
C, D, H, I	IPR003439	ABC transporter-like, ATP-binding domain	Domain
C, D, H, I	IPR003593	AAA+ ATPase domain	Domain
C, D, H, I	IPR023693	ABC transporter, vitamin B12, BtuD	Family
C, D, H, I	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, F, G	IPR037294	ABC transporter, BtuC-like	Homologous Superfamily
A, B, F, G	IPR000522	ABC transporter, permease protein, BtuC-like	Family
A, B, F, G	IPR023691	ABC transporter, vitamin B12 import, permease protein BtuC	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	OPM	Transmembrane	Alpha-helical polytopic	ABC transporters	FecCD transport family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	MemProtMD	Annotated as membrane protein by MemProtMD

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.

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