4KJZ

Crystal Structure of Thermus Thermophilus IF2, Apo and GDP-bound Forms (2-474)

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	GTP_EFTU_D2	e4kjzA9	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2	ECOD (1.6)
A	IF2_N	e4kjzA11	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: IF2_N	ECOD (1.6)
A	MnmE_helical_2nd	e4kjzA12	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MnmE_helical_2nd	ECOD (1.6)
A	IF-2	e4kjzA10	A: a/b three-layered sandwiches	X: Initiation factor IF2/eIF5b, domain 3 (From Topology)	H: Initiation factor IF2/eIF5b, domain 3 (From Topology)	T: Initiation factor IF2/eIF5b, domain 3	F: IF-2	ECOD (1.6)
B [auth D]	GTP_EFTU_D2	e4kjzD13	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2	ECOD (1.6)
B [auth D]	IF2_N	e4kjzD15	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: IF2_N	ECOD (1.6)
B [auth D]	MnmE_helical_2nd	e4kjzD16	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MnmE_helical_2nd	ECOD (1.6)
B [auth D]	IF-2	e4kjzD14	A: a/b three-layered sandwiches	X: Initiation factor IF2/eIF5b, domain 3 (From Topology)	H: Initiation factor IF2/eIF5b, domain 3 (From Topology)	T: Initiation factor IF2/eIF5b, domain 3	F: IF-2	ECOD (1.6)
C [auth B]	GTP_EFTU_D2	e4kjzB13	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2	ECOD (1.6)
C [auth B]	IF2_N	e4kjzB15	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: IF2_N	ECOD (1.6)
C [auth B]	MnmE_helical_2nd	e4kjzB16	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MnmE_helical_2nd	ECOD (1.6)
C [auth B]	IF-2	e4kjzB14	A: a/b three-layered sandwiches	X: Initiation factor IF2/eIF5b, domain 3 (From Topology)	H: Initiation factor IF2/eIF5b, domain 3 (From Topology)	T: Initiation factor IF2/eIF5b, domain 3	F: IF-2	ECOD (1.6)
D [auth C]	GTP_EFTU_D2	e4kjzC3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2	ECOD (1.6)
D [auth C]	IF2_N	e4kjzC1	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: IF2_N	ECOD (1.6)
D [auth C]	MnmE_helical_2nd	e4kjzC2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MnmE_helical_2nd	ECOD (1.6)
D [auth C]	IF-2	e4kjzC4	A: a/b three-layered sandwiches	X: Initiation factor IF2/eIF5b, domain 3 (From Topology)	H: Initiation factor IF2/eIF5b, domain 3 (From Topology)	T: Initiation factor IF2/eIF5b, domain 3	F: IF-2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.10.2480	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	6.10.250.2720	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	3.40.50.10050	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Translation initiation factor IF- 2, domain 3	CATH (4.3.0)
B [auth D]	1.10.10.2480	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
B [auth D]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B [auth D]	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B [auth D]	3.40.50.10050	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Translation initiation factor IF- 2, domain 3	CATH (4.3.0)
C [auth B]	1.10.10.2480	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
C [auth B]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C [auth B]	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
C [auth B]	3.40.50.10050	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Translation initiation factor IF- 2, domain 3	CATH (4.3.0)
D [auth C]	1.10.10.2480	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.3.0)
D [auth C]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D [auth C]	6.10.250.2720	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
D [auth C]	3.40.50.10050	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Translation initiation factor IF- 2, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth D], C [auth B], D [auth C]	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, B [auth D], C [auth B], D [auth C]	PF04760	Translation initiation factor IF-2, N-terminal region (IF2_N)	Translation initiation factor IF-2, N-terminal region	This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved. It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA s ...	This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved. It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA synthetases, and a similar fold is also found in the B5 domain of the phenylalanine-tRNA synthetase.	Domain
A, B [auth D], C [auth B], D [auth C]	PF11987	Translation-initiation factor 2 (IF-2)	Translation-initiation factor 2	IF-2 is a translation initiator in each of the three main phylogenetic domains (Eukaryotes [1], Bacteria [2] and Archaea [3]). IF2 interacts with formylmethionine-tRNA, GTP, IF1, IF3 and both ribosomal subunits [2]. Through these interactions, IF2 pr ...	IF-2 is a translation initiator in each of the three main phylogenetic domains (Eukaryotes [1], Bacteria [2] and Archaea [3]). IF2 interacts with formylmethionine-tRNA, GTP, IF1, IF3 and both ribosomal subunits [2]. Through these interactions, IF2 promotes the binding of the initiator tRNA to the A site in the smaller ribosomal subunit and catalyses the hydrolysis of GTP following initiation-complex formation [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth D], C [auth B], D [auth C]	Translation initiation factor IF-2	translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding nucleic acid binding translation initiation factor activity translation factor activity, RNA binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding nucleic acid binding translation initiation factor activity translation factor activity, RNA binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule 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	-	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth D], C [auth B], D [auth C]	IPR000178	Translation initiation factor IF-2, bacterial-like	Family
A, B [auth D], C [auth B], D [auth C]	IPR000795	Translational (tr)-type GTP-binding domain	Domain
A, B [auth D], C [auth B], D [auth C]	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
A, B [auth D], C [auth B], D [auth C]	IPR006847	Translation initiation factor IF-2, N-terminal	Domain
A, B [auth D], C [auth B], D [auth C]	IPR044145	Translation initiation factor IF-2, domain II	Domain
A, B [auth D], C [auth B], D [auth C]	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A, B [auth D], C [auth B], D [auth C]	IPR005225	Small GTP-binding protein domain	Domain
A, B [auth D], C [auth B], D [auth C]	IPR015760	Translation initiation factor IF- 2	Family
A, B [auth D], C [auth B], D [auth C]	IPR036925	Translation initiation factor IF-2, domain 3 superfamily	Homologous Superfamily
A, B [auth D], C [auth B], D [auth C]	IPR023115	Translation initiation factor IF- 2, domain 3	Domain
A, B [auth D], C [auth B], D [auth C]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.