Structure of PDB 1vy6 Chain CE

Receptor sequence

>1vy6CE (length=148) Species: 300852 (Thermus thermophilus HB8)

DFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLA
VQKAGYYARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGA
VPRAILELAGVTDILTKELGSRNPINIAYATMEALRQLRTKADVERLR

3D structure

• PDB: 1vy6 A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.
• Chain: CE
• Resolution: 2.9 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	CE	R14 T16 A17 M19 Q20 A21 G22 R24 R25 K47 P49 K57 Y61 R64 F84 G85 A86 A94 A95 T98 A102 T120 K121 E122 S125 R126 N127 N130	R10 T12 A13 M15 Q16 A17 G18 R20 R21 K43 P45 K53 Y57 R60 F80 G81 A82 A90 A91 T94 A98 T116 K117 E118 S121 R122 N123 N126
BS02	MG	CE	G85 N130	G81 N126
BS03	MG	CE	E68 D147	E64 D143

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:1vy6, PDBe:1vy6, PDBj:1vy6
• PDBsum: 1vy6
• PubMed: 25132179
• UniProt: Q5SHQ5|RS5_THET8 Small ribosomal subunit protein uS5 (Gene Name=rpsE)