Structure of PDB 1kd1 Chain K

Receptor sequence

>1kd1K (length=142) Species: 2238 (Haloarcula marismortui)

AEFDADVIVDARDCIMGRVASQVAEQALDGETVAVVNAERAVITGREEQI
VEKYEKRVDIGNDNGYFYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRV
YLGNPYDEDGEVLDGTSLDRLSNIKFVTLGEISETLGANKTW

3D structure

• PDB: 1kd1 The structures of four macrolide antibiotics bound to the large ribosomal subunit.
• Chain: K
• 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	K	I18 G20 R21 S24 L31 T47 G48 R49 Q52 K56 K59 R60 I63 N65 N67 G68 Y69 F70 P72 K73 R74 K80 T82 R84 G85 M86 P88 H89 K90 K91 R95 E99 R102 V103 Y104 K128 G140	I15 G17 R18 S21 L28 T44 G45 R46 Q49 K53 K56 R57 I60 N62 N64 G65 Y66 F67 P69 K70 R71 K77 T79 R81 G82 M83 P85 H86 K87 K88 R92 E96 R99 V100 Y101 K125 G137

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation
• GO:0017148 negative regulation of translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:1kd1, PDBe:1kd1, PDBj:1kd1
• PDBsum: 1kd1
• PubMed: 12150912
• UniProt: P29198|RL13_HALMA Large ribosomal subunit protein uL13 (Gene Name=rpl13)