1D8T

CRYSTAL STRUCTURE OF ELONGATION FACTOR, TU (EF-TU-MGGDP) COMPLEXED WITH GE2270A, A THIAZOLYL PEPTIDE ANTIBIOTIC

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1d8ta1	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	Elongation factors	Elongation factor Tu (EF-Tu), domain 2	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1d8ta2	All beta proteins	Elongation factor/aminomethyltransferase common domain	EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	Elongation factor Tu (EF-Tu)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1d8ta3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Elongation factor Tu (EF-Tu), N-terminal (G) domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1d8tb1	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	Elongation factors	Elongation factor Tu (EF-Tu), domain 2	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1d8tb2	All beta proteins	Elongation factor/aminomethyltransferase common domain	EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	Elongation factor Tu (EF-Tu)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1d8tb3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Elongation factor Tu (EF-Tu), N-terminal (G) domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8056349	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8056349	3002022	SCOP2B (2022-06-29)
B	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)

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_1	e1d8tA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
A	GTP_EFTU_D3	e1d8tA2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GTP_EFTU_D3	ECOD (1.6)
A	MnmE_helical_2nd	e1d8tA3	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	GTP_EFTU_D2_1	e1d8tB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
B	GTP_EFTU_D3	e1d8tB2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GTP_EFTU_D3	ECOD (1.6)
B	MnmE_helical_2nd	e1d8tB3	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)

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	3.40.50.300	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
A, B	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	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, B	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
A, B	ELONGATION FACTOR TU	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
C, D	THIOCILLIN GE2270	-	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus cellular process disruption of cell in another organism disruption of anatomical structure in another organism biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus cellular process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, D	BB6	Parent Component: CYS
C, D	BB7	Parent Component: CYS
C, D	BB8	Parent Component: PHE
C, D	BB9	Parent Component: CYS RESID: AA0241 , AA0242 , AA0243 , AA0244 , AA0466 , AA0467 , AA0485 , AA0541 PSI-MOD : glycine thiazole-4-carboxylic acid MOD:00246 , L-serine thiazole-4-carboxylic acid MOD:00247 , L-phenylalanine thiazole-4-carboxylic acid MOD:00248 , L-cysteine thiazole-4-carboxylic acid MOD:00249 , L-isoleucine thiazole-4-carboxylic acid MOD:01389 , L-valine thiazole-4-carboxylic acid MOD:01390 , L-threonine thiazoline-4-carboxylic acid MOD:01408 , L-glutamate thiazole-4-carboxylic acid MOD:01815
C, D	MEN	Parent Component: ASN RESID: AA0241 , AA0242 , AA0243 , AA0244 , AA0466 , AA0467 , AA0485 , AA0541 , AA0070 PSI-MOD : glycine thiazole-4-carboxylic acid MOD:00246 , L-serine thiazole-4-carboxylic acid MOD:00247 , L-phenylalanine thiazole-4-carboxylic acid MOD:00248 , L-cysteine thiazole-4-carboxylic acid MOD:00249 , L-isoleucine thiazole-4-carboxylic acid MOD:01389 , L-valine thiazole-4-carboxylic acid MOD:01390 , L-threonine thiazoline-4-carboxylic acid MOD:01408 , L-glutamate thiazole-4-carboxylic acid MOD:01815 , N4-methyl-L-asparagine MOD:00079
C, D	MH6	Parent Component: SER RESID: AA0241 , AA0242 , AA0243 , AA0244 , AA0466 , AA0467 , AA0485 , AA0541 , AA0070 , AA0540 PSI-MOD : glycine thiazole-4-carboxylic acid MOD:00246 , L-serine thiazole-4-carboxylic acid MOD:00247 , L-phenylalanine thiazole-4-carboxylic acid MOD:00248 , L-cysteine thiazole-4-carboxylic acid MOD:00249 , L-isoleucine thiazole-4-carboxylic acid MOD:01389 , L-valine thiazole-4-carboxylic acid MOD:01390 , L-threonine thiazoline-4-carboxylic acid MOD:01408 , L-glutamate thiazole-4-carboxylic acid MOD:01815 , N4-methyl-L-asparagine MOD:00079 , L-cysteine 3-hydroxy-2,5-pyridinedicarboxylic acid MOD:01814
C, D	NH2	RESID: AA0241 , AA0242 , AA0243 , AA0244 , AA0466 , AA0467 , AA0485 , AA0541 , AA0070 , AA0540 , AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : glycine thiazole-4-carboxylic acid MOD:00246 , L-serine thiazole-4-carboxylic acid MOD:00247 , L-phenylalanine thiazole-4-carboxylic acid MOD:00248 , L-cysteine thiazole-4-carboxylic acid MOD:00249 , L-isoleucine thiazole-4-carboxylic acid MOD:01389 , L-valine thiazole-4-carboxylic acid MOD:01390 , L-threonine thiazoline-4-carboxylic acid MOD:01408 , L-glutamate thiazole-4-carboxylic acid MOD:01815 , N4-methyl-L-asparagine MOD:00079 , L-cysteine 3-hydroxy-2,5-pyridinedicarboxylic acid MOD:01814 , L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109

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.