Structure of PDB 4v5d Chain AM

Receptor sequence

>4v5dAM (length=124) Species: 300852 (Thermus thermophilus HB8)

ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEA
EVVRLREYVENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQ
RTRTNARTRKGPRKTVAGKKKAPR

3D structure

• PDB: 4v5d Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome.
• Chain: AM
• 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	AM	K13 R14 V17 Y21 Y23 G24 I25 G26 K27 A28 R29 R44 V74 N77 Y87 R88 R91 H92 L96 P97 V98 R99 Q101 R102 T103 R104 T105 N106 A107 R108 T109 R110 K111 R114 K115 T116 K120 R125	K12 R13 V16 Y20 Y22 G23 I24 G25 K26 A27 R28 R43 V73 N76 Y86 R87 R90 H91 L95 P96 V97 R98 Q100 R101 T102 R103 T104 N105 A106 R107 T108 R109 K110 R113 K114 T115 K119 R124
BS02	rna	AM	T116 A118 G119	T115 A117 G118
BS03	rna	AM	A123 R125	A122 R124
BS04	rna	AM	M82 R93 R94 R125	M81 R92 R93 R124

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v5d, PDBe:4v5d, PDBj:4v5d
• PDBsum: 4v5d
• PubMed: 19363482
• UniProt: P80377|RS13_THET8 Small ribosomal subunit protein uS13 (Gene Name=rpsM)