Structure of PDB 1kd1 Chain E

Receptor sequence

>1kd1E (length=246) Species: 2238 (Haloarcula marismortui)

MQATIYDLDGNTDGEVDLPDVFETPVRSDLIGKAVRAAQANRKQDYGSDE
YAGLRTPAESFGSGRGQAHVPKLDGRARRVPQAVKGRSAHPPKTEKDRSL
DLNDKERQLAVRSALAATADADLVADRGHEFDRDEVPVVVSDDFEDLVKT
QEVVSLLEALDVHADIDRADETKIKAGQGSARGRKYRRPASILFVTSDEP
STAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTESALAEVAER

3D structure

• PDB: 1kd1 The structures of four macrolide antibiotics bound to the large ribosomal subunit.
• Chain: E
• 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	E	R27 R36 A38 N41 R42 K43 Q44 D45 Y46 G47 S48 D49 A52 G53 L54 R55 T56 P57 S60 S63 G64 G66 Q67 A68 H69 V70 L73 D74 R76 A77 R78 V80 P81 Q82 A83 V84 K85 R87 S88 H90 P92 K93 T94 E95 K96 D101 N103 D104 K105 E106 R107 R127 V148 K149 T150 Q151 R168 D170 K173 I174 K175 A176 G177 Q178 R182 R184 Y186 R187 A190 T202 R205 N206 A213 E217 V218 N219 D222 P225 G226 R246	R27 R36 A38 N41 R42 K43 Q44 D45 Y46 G47 S48 D49 A52 G53 L54 R55 T56 P57 S60 S63 G64 G66 Q67 A68 H69 V70 L73 D74 R76 A77 R78 V80 P81 Q82 A83 V84 K85 R87 S88 H90 P92 K93 T94 E95 K96 D101 N103 D104 K105 E106 R107 R127 V148 K149 T150 Q151 R168 D170 K173 I174 K175 A176 G177 Q178 R182 R184 Y186 R187 A190 T202 R205 N206 A213 E217 V218 N219 D222 P225 G226 R246

Gene Ontology

Molecular Function

• 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:1kd1, PDBe:1kd1, PDBj:1kd1
• PDBsum: 1kd1
• PubMed: 12150912
• UniProt: P12735|RL4_HALMA Large ribosomal subunit protein uL4 (Gene Name=rpl4)