Structure of PDB 8rxx Chain LD

Receptor sequence

>8rxxLD (length=175) Species: 347515 (Leishmania major strain Friedlin)

SKAANPMREIVVKKLCINICVGESGDRLTRASKVLEQLCEQTPVLSRARL
TVRTFGIRRNEKIAVHCTVRGKKAEELLEKGLKVKEFELKSYNFADTGSF
GFGIDEHIDLGIKYDPSTGIYGMDFYVVLGRRGERVAHRKRKCSRVGHSH
HVTKEEAMKWFEKVHDGIIFQAKKK

3D structure

• PDB: 8rxx Structural and mechanistic insights into the function of Leishmania ribosome lacking a single pseudouridine modification.
• Chain: LD
• Resolution: 2.97 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	LD	K18 C20 N22 C24 S50 A52 R53 F59 I61 A68 H70 Y96 N97 A99 D100 T101 G105 F106 G107 G126 M127 D128 Y130 K144 K178	K14 C16 N18 C20 S46 A48 R49 F55 I57 A64 H66 Y92 N93 A95 D96 T97 G101 F102 G103 G122 M123 D124 Y126 K140 K174
BS02	rna	LD	K6 N9 P10 M11 R12 Q45 T46 V48 T72 R74 R136 G137 R139 V140 R143 K146 S148 R149 G151 H152 H154	K2 N5 P6 M7 R8 Q41 T42 V44 T68 R70 R132 G133 R135 V136 R139 K142 S144 R145 G147 H148 H150
BS03	rna	LD	T55 R62	T51 R58

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:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8rxx, PDBe:8rxx, PDBj:8rxx
• PDBsum: 8rxx
• PubMed: 38722744
• UniProt: P48157|RL11_LEIMA Large ribosomal subunit protein uL5 (Gene Name=RPL11)