Structure of PDB 2qex Chain D

Receptor sequence

>2qexD (length=140) Species: 2238 (Haloarcula marismortui)

FHEMREPRIEKVVVHMGIGHANAEDILGEITGQMPVRTKAKRTVGEFDIR
EGDPIGAKVTLRDEMAEEFLQTALPLAELATSQFDDTGNFSFGLDVTVNL
VRPGYRVAKRDKASRSIPTKHRLNPADAVAFIESTYDVEV

3D structure

• PDB: 2qex Negamycin binds to the wall of the nascent chain exit tunnel of the 50S ribosomal subunit.
• Chain: D
• 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	D	K20 V22 H24 I27 T52 A54 R56 E60 Q97 T101 S105 F106 G107 D129 N133	K11 V13 H15 I18 T38 A40 R42 E46 Q83 T87 S91 F92 G93 D95 N99
BS02	rna	D	M13 R14 Q47 M48 P49 V50 V73 T74 R76 P137 R140 V141 K143 R144 D145 R149 P152 K154 H155	M4 R5 Q33 M34 P35 V36 V59 T60 R62 P103 R106 V107 K109 R110 D111 R115 P118 K120 H121

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:2qex, PDBe:2qex, PDBj:2qex
• PDBsum: 2qex
• PubMed: 17664317
• UniProt: P14124|RL5_HALMA Large ribosomal subunit protein uL5 (Gene Name=rpl5)