Structure of PDB 1kd1 Chain F

Receptor sequence

>1kd1F (length=140) Species: 2238 (Haloarcula marismortui)

FHEMREPRIEKVVVHMGIGHANAEDILGEITGQMPVRTKAKRTVGEFDIR
EGDPIGAKVTLRDEMAEEFLQTALPLAELATSQFDDTGNFSFGLDVTVNL
VRPGYRVAKRDKASRSIPTKHRLNPADAVAFIESTYDVEV

3D structure

• PDB: 1kd1 The structures of four macrolide antibiotics bound to the large ribosomal subunit.
• Chain: F
• 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	F	K20 V22 H24 T52 A54 K55 R56 E60 K72 Q97 D100 T101 S105 F106 G107 D129 N133 R156	K11 V13 H15 T38 A40 K41 R42 E46 K58 Q83 D86 T87 S91 F92 G93 D95 N99 R122
BS02	rna	F	E12 M13 R14 Q47 M48 V50 V73 T74 R76 P137 G138 R140 V141 R144 D145 R149 P152 K154 H155	E3 M4 R5 Q33 M34 V36 V59 T60 R62 P103 G104 R106 V107 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:1kd1, PDBe:1kd1, PDBj:1kd1
• PDBsum: 1kd1
• PubMed: 12150912
• UniProt: P14124|RL5_HALMA Large ribosomal subunit protein uL5 (Gene Name=rpl5)