Structure of PDB 5jvh Chain D

Receptor sequence

>5jvhD (length=177) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)

QLKTKYNDQVRPALMQQFGYSSVMAVPRIEKIVVNEGLGSSKEDSKAIDK
AAKELALITLQKPIITKAKKSISNFKLRQGMPVGIKVTLRGERMYVFLEK
LINIGLPRIRDFRGINPNAFDGRGNYNLGIKEQLIFPEITYDMVDKTRGM
DITIVTTAKTDEEARALLQSMGLPFRK

3D structure

• PDB: 5jvh Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding.
• Chain: D
• Resolution: 3.58 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	K33 V35 N37 G39 S42 S43 T68 K69 K71 S75 F77 V85 K88 F122 D123 R125 N127 N129 L130 G131 I132 K133 R150 D153 T155	K31 V33 N35 G37 S40 S41 T66 K67 K69 S73 F75 V83 K86 F120 D121 R123 N125 N127 L128 G129 I130 K131 R148 D151 T153
BS02	rna	D	S24 M26 A27 Q63 K64 I66 K69 T90 R92	S22 M24 A25 Q61 K62 I64 K67 T88 R90

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:5jvh, PDBe:5jvh, PDBj:5jvh
• PDBsum: 5jvh
• PubMed: 27791159
• UniProt: Q9RXJ0|RL5_DEIRA Large ribosomal subunit protein uL5 (Gene Name=rplE)