Structure of PDB 4v5d Chain DF

Receptor sequence

>4v5dDF (length=207) Species: 300852 (Thermus thermophilus HB8)

MKEVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTAS
TKTRGEVAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYT
LPKKVRKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDG
SESVLLVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWE
VFQNRIG

3D structure

• PDB: 4v5d Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome.
• Chain: DF
• Resolution: 3.5 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	DF	H31 W34 E35 R38 L41 K43 R44 R45 R46 T48 S50 T51 K52 T53 R54 V57 A58 Y59 S60 G61 R62 K63 Q67 K68 H69 G71 R72 A73 R74 H75 G76 I82 F83 V84 V88 V89 F90 P92 R95 Y99 T100 P102 K103 K104 V105 R106 K135 T136 K137 R165 R168 N169 P171 G180 N182 Y184 R205	H31 W34 E35 R38 L41 K43 R44 R45 R46 T48 S50 T51 K52 T53 R54 V57 A58 Y59 S60 G61 R62 K63 Q67 K68 H69 G71 R72 A73 R74 H75 G76 I82 F83 V84 V88 V89 F90 P92 R95 Y99 T100 P102 K103 K104 V105 R106 K135 T136 K137 R165 R168 N169 P171 G180 N182 Y184 R205
BS02	MG	DF	R168 N169 L170	R168 N169 L170

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:4v5d, PDBe:4v5d, PDBj:4v5d
• PDBsum: 4v5d
• PubMed: 19363482
• UniProt: Q5SHN9|RL4_THET8 Large ribosomal subunit protein uL4 (Gene Name=rplD)