1FKA | pdb_00001fka

STRUCTURE OF FUNCTIONALLY ACTIVATED SMALL RIBOSOMAL SUBUNIT AT 3.3 A RESOLUTION

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d1fkad_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
F	d1fkaf_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
G	d1fkag_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
I	d1fkai_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
J	d1fkaj_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
K	d1fkak_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
L	d1fkal_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
P	d1fkap_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
R	d1fkar_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
M	d1fkam_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
N	d1fkan_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
O	d1fkao_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
Q	d1fkaq_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
S	d1fkas_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d1fkab_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
T	d1fkat_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
C	d1fkac_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
E	d1fkae_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
H	d1fkah_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Small subunit	Prokaryotic (30S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G	SCOP2B Superfamily	Ribosomal protein S7	8033523	3000799	SCOP2B (2022-06-29)
S	SCOP2B Superfamily	Ribosomal protein S19	8044027	3000686	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	dsRNA-binding domain-like	8044017	3000985	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8044015	3000100	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)
D	S4	e1fkaD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Alpha-L RNA-binding motif	F: S4	ECOD (1.6)
F	Ribosomal_S6	e1fkaF1	A: a+b two layers	X: Alpha-beta plaits	H: Ribosomal protein S6 (From Topology)	T: Ribosomal protein S6	F: Ribosomal_S6	ECOD (1.6)
G	Ribosomal_S7_1	e1fkaG1	A: alpha arrays	X: Ribosomal protein S7 (From Topology)	H: Ribosomal protein S7 (From Topology)	T: Ribosomal protein S7	F: Ribosomal_S7_1	ECOD (1.6)
R	Ribosomal_S18	e1fkaR1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Ribosomal_S18	ECOD (1.6)
O	Ribosomal_S15_1	e1fkaO1	A: alpha arrays	X: S15/NS1 RNA-binding domain (From Topology)	H: S15/NS1 RNA-binding domain (From Topology)	T: S15/NS1 RNA-binding domain	F: Ribosomal_S15_1	ECOD (1.6)
S	Ribosomal_S19	e1fkaS1	A: a+b two layers	X: Ribosomal protein S19 (From Topology)	H: Ribosomal protein S19 (From Topology)	T: Ribosomal protein S19	F: Ribosomal_S19	ECOD (1.6)
E	Ribosomal_S5_C	e1fkaE2	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: Ribosomal_S5_C	ECOD (1.6)
E	Ribosomal_S5	e1fkaE1	A: a+b two layers	X: dsRBD-like	H: dsRNA-binding domain-like (From Topology)	T: dsRNA-binding domain-like	F: Ribosomal_S5	ECOD (1.6)
H	Ribosomal_S8_N	e1fkaH1	A: a+b two layers	X: R3H domain-like	H: Ribosomal protein S8, N-terminal domain (From Topology)	T: Ribosomal protein S8, N-terminal domain	F: Ribosomal_S8_N	ECOD (1.6)
H	Ribosomal_S8_C	e1fkaH2	A: a+b two layers	X: Ribosomal protein S8, C-terminal domain (From Topology)	H: Ribosomal protein S8, C-terminal domain (From Topology)	T: Ribosomal protein S8, C-terminal domain	F: Ribosomal_S8_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.1050.10	Mainly Alpha	Orthogonal Bundle	Ribosomal Protein S4 Delta 41	Chain A, domain 1	CATH (4.3.0)
D	3.10.290.10	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region	Chain A	CATH (4.3.0)
F	3.30.70.60	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Ribosomal protein S6/Translation elongation factor EF1B	CATH (4.3.0)
G	1.10.455.10	Mainly Alpha	Orthogonal Bundle	Ribosomal Protein S7	Ribosomal protein S7/S5	CATH (4.3.0)
R	4.10.640.10	Few Secondary Structures	Irregular	30s Ribosomal Protein S18	Ribosomal protein S18	CATH (4.3.0)
O	1.10.287.10	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	S15/NS1, RNA-binding	CATH (4.3.0)
S	3.30.860.10	Alpha Beta	2-Layer Sandwich	30s Ribosomal Protein S19	Chain A	CATH (4.3.0)
E	3.30.160.20	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain		CATH (4.3.0)
E	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
H	3.30.1370.30	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
H	3.30.1490.10	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF01479	S4 domain (S4)	S4 domain	The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ...	The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA.	Domain
F	PF01250	Ribosomal protein S6 (Ribosomal_S6)	Ribosomal protein S6		Domain
O	PF00312	Ribosomal protein S15 (Ribosomal_S15)	Ribosomal protein S15		Domain
E	PF03719	Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)	Ribosomal protein S5, C-terminal domain		Domain
E	PF00333	Ribosomal protein S5, N-terminal domain (Ribosomal_S5)	Ribosomal protein S5, N-terminal domain		Domain
H	PF00410	Ribosomal protein S8 (Ribosomal_S8)	Ribosomal protein S8		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	16S RIBOSOMAL RNA	-	-	-
D	30S RIBOSOMAL PROTEIN S4	structural molecule activity structural constituent of ribosome cation binding ion binding binding metal ion binding small molecule binding RNA binding rRNA binding nucleic acid binding	cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis ribosomal small subunit biogenesis biosynthetic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression macromolecule biosynthetic process	protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle ribosomal subunit intracellular organelle cellular anatomical structure ribonucleoprotein complex organelle membraneless organelle ribosome
F	30S RIBOSOMAL PROTEIN S6	RNA binding small ribosomal subunit rRNA binding binding rRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression macromolecule biosynthetic process	protein-containing complex ribonucleoprotein complex cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle ribosome
G	30S RIBOSOMAL PROTEIN S7	RNA binding binding tRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome 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 small ribosomal subunit intracellular membraneless organelle ribosomal subunit intracellular organelle cellular anatomical structure ribonucleoprotein complex organelle membraneless organelle ribosome
I	30S RIBOSOMAL PROTEIN S9	-	-	-
J	30S RIBOSOMAL PROTEIN S10	-	-	-
K	30S RIBOSOMAL PROTEIN S11	-	-	-
L	30S RIBOSOMAL PROTEIN S12	-	-	-
P	30S RIBOSOMAL PROTEIN S16	-	-	-
R	30S RIBOSOMAL PROTEIN S18	RNA binding small ribosomal subunit rRNA binding binding rRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression macromolecule biosynthetic process	protein-containing complex ribonucleoprotein complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle ribosome
M	30S RIBOSOMAL PROTEIN S13	-	-	-
N	30S RIBOSOMAL PROTEIN S14	-	-	-
O	30S RIBOSOMAL PROTEIN S15	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression macromolecule biosynthetic process	cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol
Q	30S RIBOSOMAL PROTEIN S17	-	-	-
S	30S RIBOSOMAL PROTEIN S19	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding	ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization membraneless organelle assembly ribosomal small subunit assembly protein-RNA complex assembly ribosomal small subunit biogenesis cellular component organization cellular component biogenesis ribosome biogenesis organelle organization protein-RNA complex organization cellular component assembly protein-containing complex assembly ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization membraneless organelle assembly ribosomal small subunit assembly protein-RNA complex assembly ribosomal small subunit biogenesis cellular component organization cellular component biogenesis ribosome biogenesis organelle organization protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular process cellular component organization or biogenesis ribosome assembly biosynthetic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression macromolecule biosynthetic process	protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle ribosomal subunit intracellular organelle cellular anatomical structure ribonucleoprotein complex organelle membraneless organelle ribosome cytoplasm
B	30S RIBOSOMAL PROTEIN S2	-	-	-
T	30S RIBOSOMAL PROTEIN S20	-	-	-
C	30S RIBOSOMAL PROTEIN S3	-	-	-
E	30S RIBOSOMAL PROTEIN S5	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid 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 small ribosomal subunit intracellular membraneless organelle ribosomal subunit intracellular organelle cellular anatomical structure ribonucleoprotein complex organelle membraneless organelle ribosome
H	30S RIBOSOMAL PROTEIN S8	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid 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 ribonucleoprotein complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle ribosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR018079	Small ribosomal subunit protein uS4, conserved site	Conserved Site
D	IPR002942	RNA-binding S4 domain	Domain
D	IPR001912	Small ribosomal subunit protein uS4, N-terminal	Domain
D	IPR036986	RNA-binding S4 domain superfamily	Homologous Superfamily
D	IPR005709	Small ribosomal subunit protein uS4, bacterial-type	Family
D	IPR022801	Small ribosomal subunit protein uS4	Family
F	IPR020815	Small ribosomal subunit protein bS6, conserved site	Conserved Site
F	IPR000529	Small ribosomal subunit protein bS6	Family
F	IPR020814	Small ribosomal subunit protein bS6, plastid/chloroplast	Family
F	IPR035980	Small ribosomal subunit protein bS6 superfamily	Homologous Superfamily
F	IPR014717	Translation elongation factor EF1B/small ribosomal subunit protein bS6	Homologous Superfamily
G	IPR020606	Small ribosomal subunit protein uS7, conserved site	Conserved Site
G	IPR000235	Small ribosomal subunit protein uS7	Family
G	IPR005717	Small ribosomal subunit protein uS7, bacterial/organellar-type	Family
G	IPR036823	Small ribosomal subunit protein uS7 domain superfamily	Homologous Superfamily
G	IPR023798	Small ribosomal subunit protein uS7 domain	Domain
R	IPR001648	Small ribosomal subunit protein bS18	Family
R	IPR018275	Small ribosomal subunit protein bS18, conserved site	Conserved Site
R	IPR036870	Small ribosomal subunit protein bS18 superfamily	Homologous Superfamily
O	IPR005290	Small ribosomal subunit protein uS15, bacterial-type	Family
O	IPR009068	uS15/NS1, RNA-binding domain superfamily	Homologous Superfamily
O	IPR000589	Small ribosomal subunit protein uS15	Family
S	IPR002222	Small ribosomal subunit protein uS19	Family
S	IPR005732	Small ribosomal subunit protein uS19, bacterial-type	Family
S	IPR023575	Small ribosomal subunit protein uS19, superfamily	Homologous Superfamily
S	IPR020934	Small ribosomal subunit protein uS19, conserved site	Conserved Site
E	IPR000851	Small ribosomal subunit protein uS5	Family
E	IPR005324	Small ribosomal subunit protein uS5, C-terminal	Domain
E	IPR013810	Small ribosomal subunit protein uS5, N-terminal	Domain
E	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
E	IPR018192	Small ribosomal subunit protein uS5, N-terminal, conserved site	Conserved Site
E	IPR005712	Small ribosomal subunit protein uS5, bacterial-type	Family
E	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily
H	IPR000630	Small ribosomal subunit protein uS8	Family
H	IPR047863	Small ribosomal subunit protein uS8, conserved site	Conserved Site
H	IPR035987	Small ribosomal subunit protein uS8 superfamily	Homologous Superfamily