6ZG3 | pdb_00006zg3

the structure of ECF PanT transporter in a complex with a nanobody

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
E	d6zg3e1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
E	d6zg3e2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
J	d6zg3j1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
J	d6zg3j2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	ABC_tran	e6zg3A1	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	ABC_tran	e6zg3F1	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)
G	ABC_tran	e6zg3G1	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	e6zg3B1	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)
H	ECF_trnsprt	e6zg3H1	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: ECF_trnsprt	ECOD (1.6)
C	ECF_trnsprt	e6zg3C1	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: ECF_trnsprt	ECOD (1.6)
D	CbiQ	e6zg3D1	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)
I	CbiQ	e6zg3I1	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)
E	V-set_8	e6zg3E1	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_12	e6zg3J1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
J	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E, J	Heavy Chain	IGHV1	-	energy-coupling factor transporter atp-binding proteinecfa1 \| putative cobalt abc transporter, permease protein	SAbDab (2025-06-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, F	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
B, G	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, H	PF12822	ECF transporter, substrate-specific component (ECF_trnsprt)	ECF transporter, substrate-specific component	-	Family
D, I	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, F	Energy-coupling factor transporter ATP-binding protein EcfA1	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 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	-	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
B, G	Energy-coupling factor transporter ATP-binding protein EcfA2	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 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	-	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
C, H	Conserved hypothetical membrane protein	transporter activity transmembrane transporter activity	-	cellular anatomical structure membrane
D, I	Putative cobalt ABC transporter, permease protein	transporter activity transmembrane transporter activity	-	cell periphery cellular anatomical structure plasma membrane membrane
E, J	CA14381 nanobody	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, F	IPR050095	Energy-coupling factor transporter ATP-binding	Family
A, F	IPR003593	AAA+ ATPase domain	Domain
A, F	IPR017871	ABC transporter-like, conserved site	Conserved Site
A, F	IPR015856	ABC transporter, CbiO/EcfA subunit	Domain
A, F	IPR003439	ABC transporter-like, ATP-binding domain	Domain
A, F	IPR030947	Energy-coupling factor transporter ATP-binding protein EcfA1	Family
A, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, G	IPR050095	Energy-coupling factor transporter ATP-binding	Family
B, G	IPR030946	Energy-coupling factor transporter ATP-binding protein EcfA2	Family
B, G	IPR003593	AAA+ ATPase domain	Domain
B, G	IPR017871	ABC transporter-like, conserved site	Conserved Site
B, G	IPR015856	ABC transporter, CbiO/EcfA subunit	Domain
B, G	IPR003439	ABC transporter-like, ATP-binding domain	Domain
B, G	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C, H	IPR024529	ECF transporter, substrate-specific component	Family
D, I	IPR024919	ECF transporter transmembrane protein EcfT	Family
D, I	IPR003339	ABC/ECF transporter, transmembrane component	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, F A, B, C, D, F, G, H, I	OPM	Transmembrane	Alpha-helical polytopic	Energy-coupling factor transporters	Energy-coupling factor transporters

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, F A, B, C, D, F, G, H, I	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Energy-Coupling Factor (ECF) Transporters	ECF-PanT energy-coupling factor pantothenate transporter in complex with a nanobody

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.