1OLN | pdb_00001oln

Model for thiostrepton antibiotic binding to L11 substrate from 50S ribosomal RNA

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	d1olna_	Low resolution protein structures	Computational models partly based on experimental data	Computational models partly based on experimental data	Computational models partly based on experimental data	Ribosomal L11 protein in complex with thiostrepton and a 23S rRNA fragment	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribosomal L11/L12e N-terminal domain-like	8035082	3000950	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribosomal protein L11, C-terminal domain	8036651	3001186	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	Ribosomal_L11	e1olnA1	A: alpha arrays	X: HTH	H: HTH	T: Ribosomal protein L11, C-terminal domain	F: Ribosomal_L11	ECOD (1.6)
A	Ribosomal_L11_N	e1olnA2	A: a+b two layers	X: Ribosomal protein L11/L12e N-terminal domain-like	H: Ribosomal protein L11/L12e N-terminal domain (From Topology)	T: Ribosomal protein L11/L12e N-terminal domain	F: Ribosomal_L11_N	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03946	Ribosomal protein L11, N-terminal domain (Ribosomal_L11_N)	Ribosomal protein L11, N-terminal domain	The N-terminal domain of Ribosomal protein L11 adopts an alpha/beta fold and is followed by the RNA binding C-terminal domain.	Domain
A	PF00298	Ribosomal protein L11, RNA binding domain (Ribosomal_L11)	Ribosomal protein L11, RNA binding domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	50S RIBOSOMAL PROTEIN L11	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding large ribosomal subunit rRNA binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression macromolecule biosynthetic process	protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol large ribosomal subunit
B	THIOSTREPTON	-	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 anatomical structure extracellular region
C	RNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR020785	Large ribosomal subunit protein uL11, conserved site	Conserved Site
A	IPR020783	Large ribosomal subunit protein uL11, C-terminal	Domain
A	IPR000911	Ribosomal protein uL11	Family
A	IPR036769	Large ribosomal subunit protein uL11, C-terminal domain superfamily	Homologous Superfamily
A	IPR006519	Large ribosomal subunit protein uL11, bacterial-type	Family
A	IPR020784	Large ribosomal subunit protein uL11, N-terminal	Domain
A	IPR036796	Large ribosomal subunit protein uL11, N-terminal domain superfamily	Homologous Superfamily
B	IPR023895	Thiazolylpeptide-type bacteriocin precursor	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	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
B	DBU	Parent Component: THR RESID: AA0241 , AA0242 , AA0243 , AA0244 , AA0466 , AA0467 , AA0485 , AA0541 , AA0182 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 , dehydrobutyrine (Thr) MOD:00190 , (Z)-dehydrobutyrine (Thr) MOD:01471
B	DCY	RESID: AA0241 , AA0242 , AA0243 , AA0244 , AA0466 , AA0467 , AA0485 , AA0541 , AA0182
B	DHA	Parent Component: SER RESID: AA0241 , AA0242 , AA0243 , AA0244 , AA0466 , AA0467 , AA0485 , AA0541 , AA0182 , AA0181 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 , dehydrobutyrine (Thr) MOD:00190 , (Z)-dehydrobutyrine (Thr) MOD:01471 , dehydroalanine (Ser) MOD:00189 , dehydroalanine (Cys) MOD:00793 , dehydroalanine (Tyr) MOD:00824 , dehydroalanine MOD:01168 , dehydroalanine (Sec) MOD:01954
B	MH6	Parent Component: SER RESID: AA0241 , AA0242 , AA0243 , AA0244 , AA0466 , AA0467 , AA0485 , AA0541 , AA0182 , AA0181 , 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 , dehydrobutyrine (Thr) MOD:00190 , (Z)-dehydrobutyrine (Thr) MOD:01471 , dehydroalanine (Ser) MOD:00189 , dehydroalanine (Cys) MOD:00793 , dehydroalanine (Tyr) MOD:00824 , dehydroalanine MOD:01168 , dehydroalanine (Sec) MOD:01954 , L-cysteine 3-hydroxy-2,5-pyridinedicarboxylic acid MOD:01814
B	NH2	RESID: AA0241 , AA0242 , AA0243 , AA0244 , AA0466 , AA0467 , AA0485 , AA0541 , AA0182 , AA0181 , 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 , dehydrobutyrine (Thr) MOD:00190 , (Z)-dehydrobutyrine (Thr) MOD:01471 , dehydroalanine (Ser) MOD:00189 , dehydroalanine (Cys) MOD:00793 , dehydroalanine (Tyr) MOD:00824 , dehydroalanine MOD:01168 , dehydroalanine (Sec) MOD:01954 , 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
B	QUA	RESID: AA0241 , AA0242 , AA0243 , AA0244 , AA0466 , AA0467 , AA0485 , AA0541 , AA0182 , AA0181 , AA0540 , AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 , AA0472 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 , dehydrobutyrine (Thr) MOD:00190 , (Z)-dehydrobutyrine (Thr) MOD:01471 , dehydroalanine (Ser) MOD:00189 , dehydroalanine (Cys) MOD:00793 , dehydroalanine (Tyr) MOD:00824 , dehydroalanine MOD:01168 , dehydroalanine (Sec) MOD:01954 , 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 , 4-(1-hydroxyethyl)-7-isoleucino-2-(threonin-O3-ylcarbonyl)-7,8-dihydroquinolin-8-ol MOD:01395
B	TS9	Parent Component: ILE RESID: AA0241 , AA0242 , AA0243 , AA0244 , AA0466 , AA0467 , AA0485 , AA0541 , AA0182 , AA0181 , AA0540 , AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 , AA0472

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.