Structure of PDB 6n9e Chain 2F

Receptor sequence

>6n9e2F (length=202) Species: 274 (Thermus thermophilus)

VYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRG
EVAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKV
RKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVL
LVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNR
IG

3D structure

• PDB: 6n9e Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site.
• Chain: 2F
• Resolution: 3.7 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	2F	N29 H31 L32 W34 E35 R38 Q40 L41 K43 R44 R45 R46 T48 A49 S50 K52 T53 R54 G55 V57 Y59 S60 G61 R62 K63 Q67 K68 H69 G71 R72 A73 R74 H75 G76 I82 F83 V84 G85 V89 F90 P92 P94 R95 Y99 T100 P102 K103 K104 R106 K108 K135 T136 R165 R168 N169 P171 E179 G180 Y184	N24 H26 L27 W29 E30 R33 Q35 L36 K38 R39 R40 R41 T43 A44 S45 K47 T48 R49 G50 V52 Y54 S55 G56 R57 K58 Q62 K63 H64 G66 R67 A68 R69 H70 G71 I77 F78 V79 G80 V84 F85 P87 P89 R90 Y94 T95 P97 K98 K99 R101 K103 K130 T131 R160 R163 N164 P166 E174 G175 Y179

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6n9e, PDBe:6n9e, PDBj:6n9e
• PDBsum: 6n9e
• PubMed: 30520988
• UniProt: Q5SHN9|RL4_THET8 Large ribosomal subunit protein uL4 (Gene Name=rplD)