Structure of PDB 6ndk Chain XE

Receptor sequence

>6ndkXE (length=148) Species: 300852 (Thermus thermophilus HB8)

DFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLA
VQKAGYYARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGA
VPRAILELAGVTDILTKELGSRNPINIAYATMEALRQLRTKADVERLR

3D structure

• PDB: 6ndk Importance of a tRNA anticodon loop modification and a conserved, noncanonical anticodon stem pairing intRNACGGProfor decoding
• Chain: XE
• Resolution: 3.64 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	XE	R14 T16 A17 R18 M19 Q20 A21 G22 R24 R25 F45 P49 K57 K92 A94 A95 T98 I101 A102 G103 L119 T120 K121 E122 L123 S125 R126 N127 N130	R10 T12 A13 R14 M15 Q16 A17 G18 R20 R21 F41 P45 K53 K88 A90 A91 T94 I97 A98 G99 L115 T116 K117 E118 L119 S121 R122 N123 N126

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:6ndk, PDBe:6ndk, PDBj:6ndk
• PDBsum: 6ndk
• PubMed: 30782843
• UniProt: Q5SHQ5|RS5_THET8 Small ribosomal subunit protein uS5 (Gene Name=rpsE)