Structure of PDB 6p5n Chain AF

Receptor sequence

>6p5nAF (length=225) Species: 9986 (Oryctolagus cuniculus)

NFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMAR
MARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFV
KLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNT
LIARSLGKYNIICMEDLIHEIYTVGKHFKEANNFLWPFKLSSPRGGMKKK
TTHFVEGGDAGNREDQINRLIRRMN

3D structure

• PDB: 6p5n The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs.
• Chain: AF
• Resolution: 3.2 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	AF	F24 K28 I29 R31 L32 R33 K34 F36 R45 R46 K47 Y50 H57 K58 Y60 R61 Y64 R65 I68 R69 M70 R72 M73 R75 K76 R95 G96 I97 N98 G99 P102 K103 K106 L110 R112 I116 K126 A127 N130 M131 N145 L146 K147 N150 R156 K160 K164 R165 T172 A175 G179 I184 E187 K201 N205 K211 L212 S213 S214 P215 R216 G217 G218 M219 K221 K222 R241	F2 K6 I7 R9 L10 R11 K12 F14 R23 R24 K25 Y28 H35 K36 Y38 R39 Y42 R43 I46 R47 M48 R50 M51 R53 K54 R73 G74 I75 N76 G77 P80 K81 K84 L88 R90 I94 K104 A105 N108 M109 N123 L124 K125 N128 R134 K138 K142 R143 T150 A153 G157 I162 E165 K179 N183 K189 L190 S191 S192 P193 R194 G195 G196 M197 K199 K200 R219
BS02	rna	AF	R133 E136 K221 T223 T224 H225	R111 E114 K199 T201 T202 H203

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6p5n, PDBe:6p5n, PDBj:6p5n
• PDBsum: 6p5n
• PubMed: 31609474
• UniProt: G1SV32|RL7_RABIT Large ribosomal subunit protein uL30 (Gene Name=RPL7)