Structure of PDB 2otj Chain Y

Receptor sequence

>2otjY (length=142) Species: 2238 (Haloarcula marismortui)

TELQARGLTEKTPDLSDEDARLLTQRHRVGKPQFNRQDHHKKKRVSTSWR
KPRGQLSKQRRGIKGKGDTVEAGFRSPTAVRGKHPSGFEEVRVHNVDDLE
GVDGDTEAVRIASKVGARKRERIEEEAEDAGIRVLNPTYVEV

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: Y
• 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	Y	R115 Q119 R120 H121 R122 K125 P126 Q127 F128 R130 Q131 D132 H134 K135 K136 K137 R138 V139 S142 W143 R144 K145 G148 Q149 L150 S151 K152 R154 R155 G156 I157 K158 G159 K160 V164 E165 A166 G167 F168 R169 S170 P171 T172 R175 G176 H178 P179 R186 H188 N189 R204 A206 S207 K208 V209 G210 A211 R212 K213 E215 N230 P231 Y233	R21 Q25 R26 H27 R28 K31 P32 Q33 F34 R36 Q37 D38 H40 K41 K42 K43 R44 V45 S48 W49 R50 K51 G54 Q55 L56 S57 K58 R60 R61 G62 I63 K64 G65 K66 V70 E71 A72 G73 F74 R75 S76 P77 T78 R81 G82 H84 P85 R92 H94 N95 R110 A112 S113 K114 V115 G116 A117 R118 K119 E121 N136 P137 Y139	PDBbind-CN: Kd=2nM
BS02	MG	Y	H133 K136 K137 V139	H39 K42 K43 V45

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003677 DNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006281 DNA repair
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:2otj, PDBe:2otj, PDBj:2otj
• PDBsum: 2otj
• PubMed: 17321546
• UniProt: P12736|RL32_HALMA Large ribosomal subunit protein eL32 (Gene Name=rpl32e)