Structure of PDB 4v8a Chain AF

Receptor sequence

>4v8aAF (length=201) Species: 300852 (Thermus thermophilus HB8)

VYQIPVLSPSGRREAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGE
VAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVR
KKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLL
VTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNRI
G

3D structure

• PDB: 4v8a The antibiotic thermorubin inhibits protein synthesis by binding to inter-subunit bridge b2a of the ribosome.
• Chain: AF
• Resolution: 3.2 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 L32 E35 R38 W39 Q40 L41 K43 R44 R45 R46 T48 A49 S50 T51 T53 R54 G55 V57 A58 Y59 S60 R62 K63 Q67 K68 H69 G71 R72 A73 R74 H75 G76 P81 I82 F83 V84 V88 V89 F90 P92 P94 R95 Y99 T100 P102 K103 K104 V105 R106 K108 K135 T136 R165 R168 N169 P171 G180 N182 Y184 R205	N23 H25 L26 E29 R32 W33 Q34 L35 K37 R38 R39 R40 T42 A43 S44 T45 T47 R48 G49 V51 A52 Y53 S54 R56 K57 Q61 K62 H63 G65 R66 A67 R68 H69 G70 P75 I76 F77 V78 V82 V83 F84 P86 P88 R89 Y93 T94 P96 K97 K98 V99 R100 K102 K129 T130 R159 R162 N163 P165 G174 N176 Y178 R199

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:4v8a, PDBe:4v8a, PDBj:4v8a
• PDBsum: 4v8a
• PubMed: 22240456
• UniProt: Q5SHN9|RL4_THET8 Large ribosomal subunit protein uL4 (Gene Name=rplD)