Structure of PDB 2otj Chain W

Receptor sequence

>2otjW (length=154) Species: 2238 (Haloarcula marismortui)

MHALVQLRGEVNMHTDIQDTLEMLNIHHVNHCTLVPETDAYRGMVAKVND
FVAFGEPSQETLETVLATRAEPLEGDADVDDEWVAEHTDYDDISGLAFAL
LSEETTLREQGLSPTLRLHPPRGGHDGVKHPVKEGGQLGKHDTEGIDDLL
EAMR

3D structure

• PDB: 2otj The Structures of Antibiotics Bound to the E Site Region of the 50 S Ribosomal Subunit of Haloarcula marismortui: 13-Deoxytedanolide and Girodazole.
• Chain: W
• Resolution: 2.9 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	W	R8 G9 E10 V11 N12 T15 D16 D19 T20 M23 N25 H27 H28 V29 N30 H31 D39 A40 Y41 G43 M44 K47 R69 E74 R108 R117 L118 H119 P120 P121 R122 G123 G124 H125 G127 V128 K129 R154	R8 G9 E10 V11 N12 T15 D16 D19 T20 M23 N25 H27 H28 V29 N30 H31 D39 A40 Y41 G43 M44 K47 R69 E74 R108 R117 L118 H119 P120 P121 R122 G123 G124 H125 G127 V128 K129 R154	PDBbind-CN: Kd=2nM
BS02	rna	W	R8 H14 N49 D50 K129 H130 P131 K133 E134	R8 H14 N49 D50 K129 H130 P131 K133 E134	PDBbind-CN: Kd=2nM

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006412 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:2otj, PDBe:2otj, PDBj:2otj
• PDBsum: 2otj
• PubMed: 17321546
• UniProt: P14121|RL30_HALMA Large ribosomal subunit protein uL30 (Gene Name=rpl30)