Structure of PDB 4v8e Chain AF

Receptor sequence

>4v8eAF (length=202) Species: 300852 (Thermus thermophilus HB8)

VYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRG
EVAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKV
RKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVL
LVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNR
IG

3D structure

• PDB: 4v8e A new understanding of the decoding principle on the ribosome.
• Chain: AF
• Resolution: 3.3 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	AF	N29 H31 W34 R38 W39 Q40 L41 K43 R44 R45 R46 T48 A49 S50 T51 K52 R54 G55 V57 A58 Y59 S60 G61 R62 K63 Q67 K68 H69 G71 R72 A73 R74 H75 P81 I82 F83 V84 G85 V88 V89 F90 P92 R95 Y99 T100 P102 K103 K104 V105 R106 K135 T136 K137 R165 R168 N169 P171 L176 E179 G180 N182 Y184	N24 H26 W29 R33 W34 Q35 L36 K38 R39 R40 R41 T43 A44 S45 T46 K47 R49 G50 V52 A53 Y54 S55 G56 R57 K58 Q62 K63 H64 G66 R67 A68 R69 H70 P76 I77 F78 V79 G80 V83 V84 F85 P87 R90 Y94 T95 P97 K98 K99 V100 R101 K130 T131 K132 R160 R163 N164 P166 L171 E174 G175 N177 Y179
BS02	MG	AF	R168 L170 V173	R163 L165 V168
BS03	OHX	AF	G55 V57 Y59	G50 V52 Y54

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:4v8e, PDBe:4v8e, PDBj:4v8e
• PDBsum: 4v8e
• PubMed: 22437501
• UniProt: Q5SHN9|RL4_THET8 Large ribosomal subunit protein uL4 (Gene Name=rplD)