5X41

3.5A resolution structure of a cobalt energy-coupling factor transporter using LCP method-CbiMQO

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)
C [auth M]	SCOP2B Superfamily	Gx transporter-like	8087396	3002268	SCOP2B (2022-06-29)
G [auth E]	SCOP2 Family	CbiM-like	8087395	4006594	SCOP2 (2022-06-29)
G [auth E]	SCOP2 Superfamily	Gx transporter-like	8087396	3002268	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)
A	ABC_tran	e5x41A1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ABC_tran	ECOD (1.6)
B	ABC_tran	e5x41B1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ABC_tran	ECOD (1.6)
E [auth C]	ABC_tran	e5x41C1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ABC_tran	ECOD (1.6)
F [auth D]	ABC_tran	e5x41D1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ABC_tran	ECOD (1.6)
C [auth M]	CbiM	e5x41M1	A: alpha bundles	X: Spectrin repeat-like	H: S-component of energy-coupling factor (ECF) transporters (From Topology)	T: S-component of energy-coupling factor (ECF) transporters	F: CbiM	ECOD (1.6)
G [auth E]	CbiM	e5x41E1	A: alpha bundles	X: Spectrin repeat-like	H: S-component of energy-coupling factor (ECF) transporters (From Topology)	T: S-component of energy-coupling factor (ECF) transporters	F: CbiM	ECOD (1.6)
D [auth Q]	CbiQ	e5x41Q1	A: alpha complex topology	X: T-component of energy-coupling factor (ECF) transporters (From Topology)	H: T-component of energy-coupling factor (ECF) transporters (From Topology)	T: T-component of energy-coupling factor (ECF) transporters	F: CbiQ	ECOD (1.6)
H [auth F]	CbiQ	e5x41F1	A: alpha complex topology	X: T-component of energy-coupling factor (ECF) transporters (From Topology)	H: T-component of energy-coupling factor (ECF) transporters (From Topology)	T: T-component of energy-coupling factor (ECF) transporters	F: CbiQ	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E [auth C]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
F [auth D]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, E [auth C], F [auth D]	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
C [auth M], G [auth E]	PF01891	Cobalt uptake substrate-specific transmembrane region (CbiM)	Cobalt uptake substrate-specific transmembrane region	-	Family
D [auth Q], H [auth F]	PF02361	Cobalt transport protein (CbiQ)	Cobalt transport protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, E [auth C], F [auth D]	Cobalt ABC transporter ATP-binding protein	active transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity transporter activity transmembrane transporter activity ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding active transmembrane transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity transporter activity transmembrane transporter activity ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding 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	transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization metal ion transport inorganic cation transmembrane transport cobalt ion transport transmembrane transport monoatomic cation transmembrane transport localization transition metal ion transport monoatomic ion transport cellular process monoatomic cation transport	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex cellular anatomical entity transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex
C [auth M], G [auth E]	Cobalt transport protein CbiM	cobalt ion transmembrane transporter activity monoatomic cation transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transition metal ion transmembrane transporter activity metal ion transmembrane transporter activity transmembrane transporter activity	cobalamin metabolic process cobalamin biosynthetic process water-soluble vitamin biosynthetic process tetrapyrrole metabolic process small molecule biosynthetic process cellular biosynthetic process cellular metabolic process vitamin biosynthetic process vitamin metabolic process tetrapyrrole biosynthetic process biosynthetic process small molecule metabolic process metabolic process cellular process cobalamin metabolic process cobalamin biosynthetic process water-soluble vitamin biosynthetic process tetrapyrrole metabolic process small molecule biosynthetic process cellular biosynthetic process cellular metabolic process vitamin biosynthetic process vitamin metabolic process tetrapyrrole biosynthetic process biosynthetic process small molecule metabolic process metabolic process cellular process water-soluble vitamin metabolic process	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex cellular anatomical entity transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex
D [auth Q], H [auth F]	Uncharacterized protein CbiQ	-	transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization metal ion transport inorganic cation transmembrane transport cobalt ion transport transmembrane transport monoatomic cation transmembrane transport localization transition metal ion transport monoatomic ion transport cellular process monoatomic cation transport	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex cellular anatomical entity transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, E [auth C], F [auth D]	IPR050095	Energy-coupling factor transporter ATP-binding	Family
A, B, E [auth C], F [auth D]	IPR003593	AAA+ ATPase domain	Domain
A, B, E [auth C], F [auth D]	IPR017871	ABC transporter-like, conserved site	Conserved Site
A, B, E [auth C], F [auth D]	IPR015856	ABC transporter, CbiO/EcfA subunit	Domain
A, B, E [auth C], F [auth D]	IPR005876	Cobalt transport protein ATP-binding subunit	Family
A, B, E [auth C], F [auth D]	IPR003439	ABC transporter-like, ATP-binding domain	Domain
A, B, E [auth C], F [auth D]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C [auth M], G [auth E]	IPR002751	Metal transport protein CbiM/NikMN	Family
C [auth M], G [auth E]	IPR018024	Cobalamin (vitamin B12) transport protein CbiM	Family
D [auth Q], H [auth F]	IPR052770	Cobalt transport CbiQ	Family
D [auth Q], H [auth F]	IPR003339	ABC/ECF transporter, transmembrane component	Family
D [auth Q], H [auth F]	IPR012809	Cobalt ECF transporter T component CbiQ	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C [auth M], D [auth Q], E [auth C] A, B, C [auth M], D [auth Q], E [auth C], F [auth D], G [auth E], H [auth F]	OPM				Cobalt uptake transporter

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C [auth M], D [auth Q], E [auth C] A, B, C [auth M], D [auth Q], E [auth C], F [auth D], G [auth E], H [auth F]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C [auth M], D [auth Q], E [auth C] A, B, C [auth M], D [auth Q], E [auth C], F [auth D], G [auth E], H [auth F]	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.