Structure of PDB 5fdv Chain 1G

Receptor sequence

>5fdv1G (length=181) Species: 300852 (Thermus thermophilus HB8)

PLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDAR
ILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWI
FLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDA
LRGMDIAVVTTAETDEEARALLELLGFPFRK

3D structure

• PDB: 5fdv Structure of the mammalian antimicrobial peptide Bac7(1-16) bound within the exit tunnel of a bacterial ribosome.
• Chain: 1G
• Resolution: 2.8 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	1G	K36 V38 N40 G42 L43 E45 T71 A73 I77 F80 L82 S124 D126 R128 N132 G134 L135 G154 M155 D156	K35 V37 N39 G41 L42 E44 T70 A72 I76 F79 L81 S123 D125 R127 N131 G133 L134 G153 M154 D155
BS02	rna	1G	P2 N27 V28 W29 E30 Q66 K67 A69 V70 V92 T93 R95 R96 R98	P1 N26 V27 W28 E29 Q65 K66 A68 V69 V91 T92 R94 R95 R97
BS03	MG	1G	L139 I144	L138 I143
BS04	MG	1G	N123 F125	N122 F124
BS05	MG	1G	N130 T161	N129 T160

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:5fdv, PDBe:5fdv, PDBj:5fdv
• PDBsum: 5fdv
• PubMed: 26792896
• UniProt: Q5SHQ0|RL5_THET8 Large ribosomal subunit protein uL5 (Gene Name=rplE)