Structure of PDB 1kd1 Chain O

Receptor sequence

>1kd1O (length=186) Species: 2238 (Haloarcula marismortui)

ATGPRYKVPMRRRREARTDYHQRLRLLKSGKPRLVARKSNKHVRAQLVTL
GPNGDDTLASAHSSDLAEYGWEAPTGNMPSAYLTGLLAGLRAQEAGVEEA
VLDIGLNSPTPGSKVFAIQEGAIDAGLDIPHNDDVLADWQRTRGAHIAEY
DEQLEEPLYSGDFDAADLPEHFDELRETLLDGDIEL

3D structure

• PDB: 1kd1 The structures of four macrolide antibiotics bound to the large ribosomal subunit.
• Chain: O
• Resolution: 3.0 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	O	P4 R5 Y6 K7 P9 R13 A16 T18 H21 R25 L26 K28 S29 V101 P109 P130 N132	P4 R5 Y6 K7 P9 R13 A16 T18 H21 R25 L26 K28 S29 V101 P109 P130 N132
BS02	rna	O	A1 G3 P4 Y6 V8 M10 R11 R12 R14 R17 T18 Y20 R23 R33 V35 R37 S39 N40 K41 H42 R44 Q46 N53 G54 D55 D56 T57 S60 G76 N77 M78 S108 T110 P111 S113 K114 R141 H146 I147 Y150 Q153 Y159 S160 D162	A1 G3 P4 Y6 V8 M10 R11 R12 R14 R17 T18 Y20 R23 R33 V35 R37 S39 N40 K41 H42 R44 Q46 N53 G54 D55 D56 T57 S60 G76 N77 M78 S108 T110 P111 S113 K114 R141 H146 I147 Y150 Q153 Y159 S160 D162

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:1kd1, PDBe:1kd1, PDBj:1kd1
• PDBsum: 1kd1
• PubMed: 12150912
• UniProt: P14123|RL18_HALMA Large ribosomal subunit protein uL18 (Gene Name=rpl18)