3TCF | pdb_00003tcf

Crystal structure of E. coli OppA complexed with endogenous ligands

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
H	d3tcfh_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
G	d3tcfg_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
F	d3tcff_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
E	d3tcfe_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d3tcfd_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d3tcfc_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3tcfb_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3tcfa_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Phosphate binding protein-like	8072676	4000229	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Type 2 solute binding protein-like	8072677	3000083	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)
H	Rv3651-like_N	e3tcfH3	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: Rv3651-like_N	ECOD (v295.2)
H	SBP_bac_1	e3tcfH1	A: alpha arrays	X: Alpha-lytic protease prodomain-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SBP_bac_1	ECOD (v295.2)
G	Rv3651-like_N	e3tcfG3	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: Rv3651-like_N	ECOD (v295.2)
G	SBP_bac_1	e3tcfG1	A: alpha arrays	X: Alpha-lytic protease prodomain-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SBP_bac_1	ECOD (v295.2)
F	Rv3651-like_N	e3tcfF3	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: Rv3651-like_N	ECOD (v295.2)
F	SBP_bac_1	e3tcfF1	A: alpha arrays	X: Alpha-lytic protease prodomain-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SBP_bac_1	ECOD (v295.2)
E	Rv3651-like_N	e3tcfE3	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: Rv3651-like_N	ECOD (v295.2)
E	SBP_bac_1	e3tcfE2	A: alpha arrays	X: Alpha-lytic protease prodomain-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SBP_bac_1	ECOD (v295.2)
D	Rv3651-like_N	e3tcfD3	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: Rv3651-like_N	ECOD (v295.2)
D	SBP_bac_1	e3tcfD2	A: alpha arrays	X: Alpha-lytic protease prodomain-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SBP_bac_1	ECOD (v295.2)
C	Rv3651-like_N	e3tcfC3	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: Rv3651-like_N	ECOD (v295.2)
C	SBP_bac_1	e3tcfC1	A: alpha arrays	X: Alpha-lytic protease prodomain-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SBP_bac_1	ECOD (v295.2)
B	Rv3651-like_N	e3tcfB3	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: Rv3651-like_N	ECOD (v295.2)
B	SBP_bac_1	e3tcfB1	A: alpha arrays	X: Alpha-lytic protease prodomain-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SBP_bac_1	ECOD (v295.2)
A	Rv3651-like_N	e3tcfA3	A: alpha arrays	X: HTH	H: HTH	T: winged helix domain	F: Rv3651-like_N	ECOD (v295.2)
A	SBP_bac_1	e3tcfA1	A: alpha arrays	X: Alpha-lytic protease prodomain-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SBP_bac_1	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
H	3.90.76.10	Alpha Beta	Alpha-Beta Complex	Dipeptide-binding Protein	domain 1	CATH (4.3.0)
H	3.10.105.10	Alpha Beta	Roll	Dipeptide-binding Protein	domain 3	CATH (4.3.0)
G	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
G	3.90.76.10	Alpha Beta	Alpha-Beta Complex	Dipeptide-binding Protein	domain 1	CATH (4.3.0)
G	3.10.105.10	Alpha Beta	Roll	Dipeptide-binding Protein	domain 3	CATH (4.3.0)
F	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
F	3.90.76.10	Alpha Beta	Alpha-Beta Complex	Dipeptide-binding Protein	domain 1	CATH (4.3.0)
F	3.10.105.10	Alpha Beta	Roll	Dipeptide-binding Protein	domain 3	CATH (4.3.0)
E	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
E	3.90.76.10	Alpha Beta	Alpha-Beta Complex	Dipeptide-binding Protein	domain 1	CATH (4.3.0)
E	3.10.105.10	Alpha Beta	Roll	Dipeptide-binding Protein	domain 3	CATH (4.3.0)
D	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
D	3.90.76.10	Alpha Beta	Alpha-Beta Complex	Dipeptide-binding Protein	domain 1	CATH (4.3.0)
D	3.10.105.10	Alpha Beta	Roll	Dipeptide-binding Protein	domain 3	CATH (4.3.0)
C	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
C	3.90.76.10	Alpha Beta	Alpha-Beta Complex	Dipeptide-binding Protein	domain 1	CATH (4.3.0)
C	3.10.105.10	Alpha Beta	Roll	Dipeptide-binding Protein	domain 3	CATH (4.3.0)
B	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
B	3.90.76.10	Alpha Beta	Alpha-Beta Complex	Dipeptide-binding Protein	domain 1	CATH (4.3.0)
B	3.10.105.10	Alpha Beta	Roll	Dipeptide-binding Protein	domain 3	CATH (4.3.0)
A	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
A	3.90.76.10	Alpha Beta	Alpha-Beta Complex	Dipeptide-binding Protein	domain 1	CATH (4.3.0)
A	3.10.105.10	Alpha Beta	Roll	Dipeptide-binding Protein	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I, J, K, L, M I, J, K, L, M, N, O, P	Endogenous peptide	-	-	-
A, B, C, D, E A, B, C, D, E, F, G, H	Periplasmic oligopeptide-binding protein	peptide transmembrane transporter activity transporter activity transmembrane transporter activity binding oligopeptide binding	peptide transport localization transport establishment of localization import into cell nitrogen compound transport oligopeptide transport import across plasma membrane transmembrane transport oligopeptide transmembrane transport oligopeptide import across plasma membrane cellular process response to stimulus response to stress peptide transport localization transport establishment of localization import into cell nitrogen compound transport oligopeptide transport import across plasma membrane transmembrane transport oligopeptide transmembrane transport oligopeptide import across plasma membrane cellular process response to stimulus response to stress response to heat response to abiotic stimulus response to temperature stimulus	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 extracellular region periplasmic space 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 extracellular region periplasmic space outer membrane-bounded periplasmic space cell envelope

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR030678	Peptide/nickel binding protein, MppA-type	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR023765	Solute-binding protein family 5, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000914	Solute-binding protein family 5 domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR039424	Solute-binding protein family 5	Family