2HDN | pdb_00002hdn

Trypsin-modified Elongation Factor Tu in complex with tetracycline at 2.8 Angstrom resolution

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J	SCOP2B Superfamily	EF-Tu post-G domain-like	8056350	3002024	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	EF-Tu post-G domain-like	8056352	3002024	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	EF-Tu post-G domain-like	8056350	3002024	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	EF-Tu post-G domain-like	8056352	3002024	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	EF-Tu post-G domain-like	8056352	3002024	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	EF-Tu post-G domain-like	8056350	3002024	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	EF-Tu post-G domain-like	8056350	3002024	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	EF-Tu post-G domain-like	8056352	3002024	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	EF-Tu post-G domain-like	8056350	3002024	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	EF-Tu post-G domain-like	8056352	3002024	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EF-Tu post-G domain-like	8056350	3002024	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EF-Tu post-G domain-like	8056352	3002024	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
J		e2hdnJ2	A: alpha bundles	X: YrdC/RibB	H: YrdC/RibB	T: YrdC/RibB	F:	ECOD (develop294)
L	Inhibitor_I9	e2hdnL2	A: alpha bundles	X: alpha/beta-Hydrolases	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: Inhibitor_I9	ECOD (develop294)
L	Acetyltransf_9	e2hdnL4	A: alpha bundles	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Acetyltransf_9	ECOD (develop294)
H	Inhibitor_I9	e2hdnH2	A: alpha bundles	X: alpha/beta-Hydrolases	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: Inhibitor_I9	ECOD (develop294)
H	Acetyltransf_9	e2hdnH4	A: alpha bundles	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Acetyltransf_9	ECOD (develop294)
F	Inhibitor_I9	e2hdnF2	A: alpha bundles	X: alpha/beta-Hydrolases	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: Inhibitor_I9	ECOD (develop294)
F	Acetyltransf_9	e2hdnF4	A: alpha bundles	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Acetyltransf_9	ECOD (develop294)
D	Inhibitor_I9	e2hdnD2	A: alpha bundles	X: alpha/beta-Hydrolases	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: Inhibitor_I9	ECOD (develop294)
D	Acetyltransf_9	e2hdnD4	A: alpha bundles	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Acetyltransf_9	ECOD (develop294)
B	Inhibitor_I9	e2hdnB2	A: alpha bundles	X: alpha/beta-Hydrolases	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: Inhibitor_I9	ECOD (develop294)
B	Acetyltransf_9	e2hdnB4	A: alpha bundles	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Acetyltransf_9	ECOD (develop294)
K	Granulin	e2hdnK01	A: alpha bundles	X: Caspase-like	H: Caspase-like	T: Caspase-like	F: Granulin	ECOD (develop294)
I	Granulin	e2hdnI01	A: alpha bundles	X: Caspase-like	H: Caspase-like	T: Caspase-like	F: Granulin	ECOD (develop294)
G	Granulin	e2hdnG01	A: alpha bundles	X: Caspase-like	H: Caspase-like	T: Caspase-like	F: Granulin	ECOD (develop294)
E	Granulin	e2hdnE01	A: alpha bundles	X: Caspase-like	H: Caspase-like	T: Caspase-like	F: Granulin	ECOD (develop294)
C	Granulin	e2hdnC01	A: alpha bundles	X: Caspase-like	H: Caspase-like	T: Caspase-like	F: Granulin	ECOD (develop294)
A	Granulin	e2hdnA01	A: alpha bundles	X: Caspase-like	H: Caspase-like	T: Caspase-like	F: Granulin	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
J	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
L	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
L	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
H	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
H	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
F	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H, J B, D, F, H, J, L	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
B, D, F, H, J B, D, F, H, J, L	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
B, D, F, H, J B, D, F, H, J, L	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L	Elongation factor EF-Tu	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding guanosine tetraphosphate binding guanyl nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding purine nucleotide binding anion binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding guanosine tetraphosphate binding guanyl nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding translation factor activity translation elongation factor activity RNA binding nucleic acid 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 primary metabolic process translation gene expression macromolecule biosynthetic process protein biosynthetic process biosynthetic process translational elongation metabolic process cellular process macromolecule metabolic process protein metabolic process	cell periphery cellular anatomical structure plasma membrane membrane intracellular anatomical structure cytoplasm protein-containing complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex
A, C, E, G, I A, C, E, G, I, K	Elongation factor EF-Tu	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding guanosine tetraphosphate binding guanyl nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding purine nucleotide binding anion binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding guanosine tetraphosphate binding guanyl nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding translation factor activity translation elongation factor activity RNA binding nucleic acid 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 primary metabolic process translation gene expression macromolecule biosynthetic process protein biosynthetic process biosynthetic process translational elongation metabolic process cellular process macromolecule metabolic process protein metabolic process	cell periphery cellular anatomical structure plasma membrane membrane intracellular anatomical structure cytoplasm protein-containing complex guanyl-nucleotide exchange factor complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L	IPR005225	Small GTP-binding domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR000795	Translational (tr)-type GTP-binding domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR033720	Elongation factor Tu, domain 2	Domain
B, D, F, H, J B, D, F, H, J, L	IPR009001	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR031157	Tr-type G domain, conserved site	Conserved Site
B, D, F, H, J B, D, F, H, J, L	IPR004541	Translation elongation factor EFTu/EF1A, bacterial/organelle	Family
B, D, F, H, J B, D, F, H, J, L	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
B, D, F, H, J B, D, F, H, J, L	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR004160	Translation elongation factor EFTu/EF1A, C-terminal	Domain
B, D, F, H, J B, D, F, H, J, L	IPR050055	Elongation factor Tu GTPase	Family
B, D, F, H, J B, D, F, H, J, L	IPR041709	Elongation factor Tu (EF-Tu), GTP-binding domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR005225	Small GTP-binding domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR000795	Translational (tr)-type GTP-binding domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR033720	Elongation factor Tu, domain 2	Domain
A, C, E, G, I A, C, E, G, I, K	IPR009001	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR031157	Tr-type G domain, conserved site	Conserved Site
A, C, E, G, I A, C, E, G, I, K	IPR004541	Translation elongation factor EFTu/EF1A, bacterial/organelle	Family
A, C, E, G, I A, C, E, G, I, K	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
A, C, E, G, I A, C, E, G, I, K	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR004160	Translation elongation factor EFTu/EF1A, C-terminal	Domain
A, C, E, G, I A, C, E, G, I, K	IPR050055	Elongation factor Tu GTPase	Family
A, C, E, G, I A, C, E, G, I, K	IPR041709	Elongation factor Tu (EF-Tu), GTP-binding domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily