4KJZ | pdb_00004kjz

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)
D [auth C]		e4kjzC1	A: Single-stranded left-handed beta-helix	X: Immunoglobulin-related	H: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	T: JmjC_2	F:	ECOD (20:10:01)
D [auth C]		e4kjzC4	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Class I glutamine amidotransferase-like	T:	F:	ECOD (20:10:01)
C [auth B]		e4kjzB13	A: Glutamine synthetase-like	X: Glutamine synthetase/guanido kinase	H: Glutamine synthetase/guanido kinase	T: PGM_PMM_I	F:	ECOD (20:10:01)
B [auth D]		e4kjzD13	A: Glutamine synthetase-like	X: Glutamine synthetase/guanido kinase	H: Glutamine synthetase/guanido kinase	T: PGM_PMM_I	F:	ECOD (20:10:01)
A		e4kjzA9	A: Glutamine synthetase-like	X: Glutamine synthetase/guanido kinase	H: Glutamine synthetase/guanido kinase	T: PGM_PMM_I	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)

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]	PF22042	Elongation factor G domain 2 (EF-G_D2)	Elongation factor G domain 2	Elongation factor G (EF-G) catalyzes the translocation step of translation. It consists of five structural domains, this entry represents the second domain [1]. This domain adopts a beta barrel structure. This family also includes domains found in ot ...	Elongation factor G (EF-G) catalyzes the translocation step of translation. It consists of five structural domains, this entry represents the second domain [1]. This domain adopts a beta barrel structure. This family also includes domains found in other translation factors such as translation initiation factor IF-2, peptide chain release factor, etc.	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 factor activity translation initiation factor activity 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 translation factor activity translation initiation factor activity 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	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth D], C [auth B], D [auth C]	IPR005225	Small GTP-binding domain	Domain
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]	IPR053905	Elongation factor G-like, domain II	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]	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 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.