Structure of PDB 4ji7 Chain D

Receptor sequence

>4ji7D (length=208) Species: 300852 (Thermus thermophilus HB8)

GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRP
SDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRL
DNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEK
SRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQ
LVIEFYSR

3D structure

• PDB: 4ji7 The central role of protein S12 in organizing the structure of the decoding site of the ribosome.
• Chain: D
• Resolution: 3.5 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 I5 P7 V8 R10 R13 R14 K22 E24 R25 K30 R35 R36 Y38 P40 G41 Q42 H43 K46 S52 Y54 A55 L58 R59 K61 Q62 E72 R73 Q74 K84 K86 G87 S113 Q116 Q119 R122 H123 H125 R132 V133 D134 L135 P136 S137 Y138 K151 L155 R209	G1 R2 I4 P6 V7 R9 R12 R13 K21 E23 R24 K29 R34 R35 Y37 P39 G40 Q41 H42 K45 S51 Y53 A54 L57 R58 K60 Q61 E71 R72 Q73 K83 K85 G86 S112 Q115 Q118 R121 H122 H124 R131 V132 D133 L134 P135 S136 Y137 K150 L154 R208
BS02	MG	D	S83 T89	S82 T88

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:4ji7, PDBe:4ji7, PDBj:4ji7
• PDBsum: 4ji7
• PubMed: 24152548
• UniProt: P80373|RS4_THET8 Small ribosomal subunit protein uS4 (Gene Name=rpsD)