4P3Y

Crystal structure of Acinetobacter baumannii DsbA in complex with EF-Tu

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)
A	d4p3ya2	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	automated matches	automated matches	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
A	d4p3ya3	All beta proteins	Elongation factor/aminomethyltransferase common domain	EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	automated matches	automated matches	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
A	d4p3ya1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
B	d4p3yb1	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	automated matches	automated matches	(Acinetobacter baumannii AYE ) [TaxId: 509173 ],	SCOPe (2.08)
B	d4p3yb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Acinetobacter baumannii AYE ) [TaxId: 509173 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8056349	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-Tu post-G domain-like	8056350	3002024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-Tu post-G domain-like	8056352	3002024	SCOP2B (2022-06-29)
B	SCOP2 Family	DsbA-like	8080061	4000595	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Thioredoxin-like	8080062	3000031	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	PF03144	e4p3yA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PF03144	ECOD (1.6)
A	PF03143	e4p3yA3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: PF03143	ECOD (1.6)
A	PF00009	e4p3yA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00009	ECOD (1.6)
B	F_UNCLASSIFIED	e4p3yB2	A: alpha arrays	X: Insertion subdomain in DsbA-like	H: Insertion subdomain in DsbA-like (From Topology)	T: Insertion subdomain in DsbA-like	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF01323	e4p3yB1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: PF01323	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)
A	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00009	Elongation factor Tu GTP binding domain (GTP_EFTU)	Elongation factor Tu GTP binding domain	This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.	Domain
A	PF03143	Elongation factor Tu C-terminal domain (GTP_EFTU_D3)	Elongation factor Tu C-terminal domain	Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA [1] and binding to EF-Ts Pfam:PF00889 [2].	Domain
A	PF03144	Elongation factor Tu domain 2 (GTP_EFTU_D2)	Elongation factor Tu domain 2	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as e ...	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to Pfam:PF03143, and in fact has weak sequence matches to this domain.	Domain
B	PF01323	DSBA-like thioredoxin domain (DSBA)	DSBA-like thioredoxin domain	This family contains a diverse set of proteins with a thioredoxin-like structure Pfam:PF00085. This family also includes 2-hydroxychromene-2-carboxylate (HCCA) isomerase enzymes catalyse one step in prokaryotic polyaromatic hydrocarbon (PAH) cataboli ...	This family contains a diverse set of proteins with a thioredoxin-like structure Pfam:PF00085. This family also includes 2-hydroxychromene-2-carboxylate (HCCA) isomerase enzymes catalyse one step in prokaryotic polyaromatic hydrocarbon (PAH) catabolic pathways [2,3,4]. This family also contains members with functions other than HCCA isomerisation, such as Kappa family GSTs (e.g. Swiss:P24473), whose similarity to HCCA isomerases was not previously recognised. The sequence Swiss:O07298 has been annotated as a dioxygenase but is almost certainly an HCCA isomerase enzyme. Similarly, the sequence Swiss:Q9ZI67 has been annotated as a dehydrogenase, but is most probably also an HCCA isomerase enzyme. In addition, the Rhizobium leguminosarum Swiss:Q52782 protein has been annotated as a putative glycerol-3-phosphate transfer protein, but is also most likely to be an HCCA isomerase enzyme (see [5]).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Elongation factor Tu 1	guanosine tetraphosphate binding guanyl nucleotide binding binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding guanosine tetraphosphate binding guanyl nucleotide binding binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding translation regulator activity translation regulator activity, nucleic acid binding translation elongation factor activity nucleic acid binding translation factor activity, RNA binding RNA binding GTP binding purine ribonucleoside triphosphate binding pyrophosphatase activity GTPase 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	response to stimulus response to chemical response to antibiotic organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation gene expression macromolecule biosynthetic process organic substance metabolic process biosynthetic process translational elongation response to stimulus response to chemical response to antibiotic organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation gene expression macromolecule biosynthetic process organic substance metabolic process biosynthetic process translational elongation organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process	cell periphery plasma membrane membrane cellular anatomical entity intracellular anatomical structure cytoplasm protein-containing complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex
B	Thiol:disulfide interchange protein	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000795	Translational (tr)-type GTP-binding domain	Domain
A	IPR033720	Elongation factor Tu, domain 2	Domain
A	IPR009001	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal	Homologous Superfamily
A	IPR031157	Tr-type G domain, conserved site	Conserved Site
A	IPR004541	Translation elongation factor EFTu/EF1A, bacterial/organelle	Family
A	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
A	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A	IPR004160	Translation elongation factor EFTu/EF1A, C-terminal	Domain
A	IPR005225	Small GTP-binding protein domain	Domain
A	IPR041709	Elongation factor Tu (EF-Tu), GTP-binding domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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 R01GM133198.