Structure of PDB 4v8d Chain DP

Receptor sequence

>4v8dDP (length=141) Species: 300852 (Thermus thermophilus HB8)

MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDYGLVALEPAWITAQQIEAA
RVAMVRHFRRGGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPG
RVMFEVAGVTEEQAMEALRIAGHKLPIKTKIVRRDAYDEAQ

3D structure

• PDB: 4v8d A new understanding of the decoding principle on the ribosome.
• Chain: DP
• Resolution: 3.0 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	DP	R51 R56	R51 R56
BS02	rna	DP	R5 R6 M7 K8 Y9 K11 Q12 Q13 R14 G15 R16 K22 G23 G24 Y26 A40 W41 Q46 A49 R56 I66 R67 F69 D71 Y74 K77 E80 V81 R82 M83 G84 K85 G86 K87 G88 R101 R119 H123 K124 P126 K128 A140 Q141	R5 R6 M7 K8 Y9 K11 Q12 Q13 R14 G15 R16 K22 G23 G24 Y26 A40 W41 Q46 A49 R56 I66 R67 F69 D71 Y74 K77 E80 V81 R82 M83 G84 K85 G86 K87 G88 R101 R119 H123 K124 P126 K128 A140 Q141
BS03	rna	DP	R16 K18	R16 K18

Gene Ontology

Molecular Function

• GO:0000049 tRNA 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:4v8d, PDBe:4v8d, PDBj:4v8d
• PDBsum: 4v8d
• PubMed: 22437501
• UniProt: P60489|RL16_THET8 Large ribosomal subunit protein uL16 (Gene Name=rplP)