Structure of PDB 1ibk Chain D

Receptor sequence

>1ibkD (length=208) Species: 274 (Thermus thermophilus)

GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRP
SDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRL
DNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEK
SRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQ
LVIEFYSR

3D structure

• PDB: 1ibk Recognition of cognate transfer RNA by the 30S ribosomal subunit.
• Chain: D
• Resolution: 3.31 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	D	G2 R3 P7 V8 C9 R10 R13 R14 K22 E24 R25 K30 R35 R36 Y38 P40 G41 Q42 H43 Q45 S52 A55 R59 Q62 E72 R73 Q74 S113 R115 Q116 Q119 R122 H123 H125 V133 D134 L135 S137 Y138 L155 E156 E205 R209	G1 R2 P6 V7 C8 R9 R12 R13 K21 E23 R24 K29 R34 R35 Y37 P39 G40 Q41 H42 Q44 S51 A54 R58 Q61 E71 R72 Q73 S112 R114 Q115 Q118 R121 H122 H124 V132 D133 L134 S136 Y137 L154 E155 E204 R208
BS02	MG	D	A82 S83 K85 T89	A81 S82 K84 T88
BS03	ZN	D	C26 C31	C25 C30

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006412 translation
• GO:0042274 ribosomal small subunit biogenesis

Cellular Component

• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:1ibk, PDBe:1ibk, PDBj:1ibk
• PDBsum: 1ibk
• PubMed: 11340196
• UniProt: P80373|RS4_THET8 Small ribosomal subunit protein uS4 (Gene Name=rpsD)