8Z1Y | pdb_00008z1y

Cryo-EM structure of Escherichia coli DppABCDF in the pre-catalytic state

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth F]	SCOP2B Superfamily	Type 2 solute binding protein-like	8033354	3000083	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth F]	PF00496	Bacterial extracellular solute-binding proteins, family 5 Middle (SBP_bac_5)	Bacterial extracellular solute-binding proteins, family 5 Middle	The borders of this family are based on the PDBSum definitions of the domain edges for Swiss:P06202.	Domain
D	PF08352	Oligopeptide/dipeptide transporter, C-terminal region (oligo_HPY)	Oligopeptide/dipeptide transporter, C-terminal region	-	Family
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	PF08352	Oligopeptide/dipeptide transporter, C-terminal region (oligo_HPY)	Oligopeptide/dipeptide transporter, C-terminal region	-	Family
C	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	PF00528	Binding-protein-dependent transport system inner membrane component (BPD_transp_1)	Binding-protein-dependent transport system inner membrane component	-	Family
B	PF12911	N-terminal TM domain of oligopeptide transport permease C (OppC_N)	N-terminal TM domain of oligopeptide transport permease C	Oligopeptide permeases (Opp) have been identified in numerous gram-negative and -positive bacteria. These transport systems belong to the superfamily of highly conserved ATP-binding cassette transporters. Typically, Opp importers comprise a complex o ...	Oligopeptide permeases (Opp) have been identified in numerous gram-negative and -positive bacteria. These transport systems belong to the superfamily of highly conserved ATP-binding cassette transporters. Typically, Opp importers comprise a complex of five proteins. The oligopeptide-binding protein OppA is responsible for the capture of peptides from the external medium. Two integral highly hydrophobic membrane spanning proteins, OppB and OppC, form a channel through the membrane used for peptide translocation. This N-terminal domain appears to be the first TM domain of the molecule [1].	Domain
A	PF00528	Binding-protein-dependent transport system inner membrane component (BPD_transp_1)	Binding-protein-dependent transport system inner membrane component	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth F]	Dipeptide-binding protein	peptide transmembrane transporter activity transporter activity transmembrane transporter activity binding tetrapyrrole binding heme binding dipeptide transmembrane transporter activity oligopeptide transmembrane transporter activity amide transmembrane transporter activity peptide binding	nitrogen compound transport transport iron ion transport establishment of localization metal ion transport localization heme transport transition metal ion transport monoatomic ion transport monoatomic cation transport iron coordination entity transport establishment of protein localization protein transport macromolecule localization nitrogen compound transport transport iron ion transport establishment of localization metal ion transport localization heme transport transition metal ion transport monoatomic ion transport monoatomic cation transport iron coordination entity transport establishment of protein localization protein transport macromolecule localization intracellular protein localization peptide transport dipeptide transport amide transport oligopeptide transport positive chemotaxis chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion heme transmembrane transport monoatomic ion transmembrane transport iron ion transmembrane transport monoatomic cation transmembrane transport transmembrane transport cellular process	cellular anatomical structure membrane ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex outer membrane-bounded periplasmic space cell envelope cellular anatomical structure membrane ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex outer membrane-bounded periplasmic space cell envelope periplasmic space
D	Dipeptide transport ATP-binding protein DppF	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 heme transmembrane transporter activity transporter activity transmembrane transporter 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 ATP-dependent activity dipeptide transmembrane transporter activity oligopeptide transmembrane transporter activity amide transmembrane transporter activity	localization establishment of protein localization nitrogen compound transport protein transport transport macromolecule localization intracellular protein localization establishment of localization response to stimulus response to radiation response to abiotic stimulus peptide transport dipeptide transport amide transport localization establishment of protein localization nitrogen compound transport protein transport transport macromolecule localization intracellular protein localization establishment of localization response to stimulus response to radiation response to abiotic stimulus peptide transport dipeptide transport amide transport oligopeptide transport heme transmembrane transport monoatomic ion transmembrane transport iron ion transport iron ion transmembrane transport metal ion transport monoatomic cation transmembrane transport transmembrane transport heme transport transition metal ion transport monoatomic ion transport cellular process monoatomic cation transport iron coordination entity transport	cellular anatomical structure membrane ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex
C	Dipeptide transport ATP-binding protein DppD	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 heme transmembrane transporter activity transporter activity transmembrane transporter 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 ATP-dependent activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding	localization establishment of protein localization nitrogen compound transport protein transport transport macromolecule localization intracellular protein localization establishment of localization peptide transport dipeptide transport amide transport oligopeptide transport heme transmembrane transport monoatomic ion transmembrane transport localization establishment of protein localization nitrogen compound transport protein transport transport macromolecule localization intracellular protein localization establishment of localization peptide transport dipeptide transport amide transport oligopeptide transport heme transmembrane transport monoatomic ion transmembrane transport iron ion transport iron ion transmembrane transport metal ion transport monoatomic cation transmembrane transport transmembrane transport heme transport transition metal ion transport monoatomic ion transport cellular process monoatomic cation transport iron coordination entity transport	cellular anatomical structure membrane ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex
B	Dipeptide transport system permease protein DppC	dipeptide transmembrane transporter activity oligopeptide transmembrane transporter activity amide transmembrane transporter activity transporter activity transmembrane transporter activity	peptide transport localization nitrogen compound transport dipeptide transport amide transport transport oligopeptide transport establishment of localization heme transmembrane transport monoatomic ion transmembrane transport iron ion transport iron ion transmembrane transport metal ion transport monoatomic cation transmembrane transport peptide transport localization nitrogen compound transport dipeptide transport amide transport transport oligopeptide transport establishment of localization heme transmembrane transport monoatomic ion transmembrane transport iron ion transport iron ion transmembrane transport metal ion transport monoatomic cation transmembrane transport transmembrane transport heme transport transition metal ion transport monoatomic ion transport cellular process monoatomic cation transport iron coordination entity transport establishment of protein localization protein transport macromolecule localization intracellular protein localization	ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing 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
A	Dipeptide transport system permease protein DppB	dipeptide transmembrane transporter activity oligopeptide transmembrane transporter activity amide transmembrane transporter activity transporter activity transmembrane transporter activity	peptide transport localization nitrogen compound transport dipeptide transport amide transport transport oligopeptide transport establishment of localization heme transmembrane transport monoatomic ion transmembrane transport iron ion transport iron ion transmembrane transport metal ion transport monoatomic cation transmembrane transport peptide transport localization nitrogen compound transport dipeptide transport amide transport transport oligopeptide transport establishment of localization heme transmembrane transport monoatomic ion transmembrane transport iron ion transport iron ion transmembrane transport metal ion transport monoatomic cation transmembrane transport transmembrane transport heme transport transition metal ion transport monoatomic ion transport cellular process monoatomic cation transport iron coordination entity transport establishment of protein localization protein transport macromolecule localization intracellular protein localization	ATPase dependent transmembrane transport complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth F]	IPR030678	Peptide/nickel binding protein, MppA-type	Family
E [auth F]	IPR023765	Solute-binding protein family 5, conserved site	Conserved Site
E [auth F]	IPR000914	Solute-binding protein family 5 domain	Domain
E [auth F]	IPR050017	Dipeptide ABC transporter periplasmic-binding protein DppA	Family
E [auth F]	IPR039424	Solute-binding protein family 5	Family
D	IPR017871	ABC transporter-like, conserved site	Conserved Site
D	IPR013563	Oligopeptide/dipeptide ABC transporter, C-terminal	Domain
D	IPR003439	ABC transporter-like, ATP-binding domain	Domain
D	IPR003593	AAA+ ATPase domain	Domain
D	IPR050021	Dipeptide ABC transporter ATP-binding subunit DppF	Family
D	IPR050319	ABC Transporter ATP-Binding	Family
D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C	IPR017871	ABC transporter-like, conserved site	Conserved Site
C	IPR013563	Oligopeptide/dipeptide ABC transporter, C-terminal	Domain
C	IPR003439	ABC transporter-like, ATP-binding domain	Domain
C	IPR050388	ABC Transporter, Nickel and Peptide Import	Family
C	IPR003593	AAA+ ATPase domain	Domain
C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B	IPR025966	Oligopeptide transport permease C-like, N-terminal domain	Domain
B	IPR050366	Binding-protein-dependent transport system permease	Family
B	IPR000515	ABC transporter type 1, transmembrane domain MetI-like	Domain
B	IPR035906	MetI-like superfamily	Homologous Superfamily
A	IPR000515	ABC transporter type 1, transmembrane domain MetI-like	Domain
A	IPR035906	MetI-like superfamily	Homologous Superfamily
A	IPR045621	ABC transporter type 1, GsiC-like, N-terminal domain	Domain