Structure of PDB 5vp2 Chain 1l

Receptor sequence

>5vp21l (length=122) Species: 300852 (Thermus thermophilus HB8)

PTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRK
VAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGV
YDAAGVKDRKKSRSKYGTKKPK

3D structure

• PDB: 5vp2 Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state.
• Chain: 1l
• Resolution: 2.8 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	1l	P5 T6 N8 Q9 R12 R15 E16 A30 P31 F32 R33 R34 K46 K47 N49 S50 L52 R53 K54 T61 Y69 G72 E73 L84 G87 V90 K91 X92 R97 R113 K114 K115 S116 R117 S118 K119 Y120 T122 K123 K124	P1 T2 N4 Q5 R8 R11 E12 A26 P27 F28 R29 R30 K42 K43 N45 S46 L48 R49 K50 T57 Y65 G68 E69 L80 G83 V86 K87 X88 R93 R109 K110 K111 S112 R113 S114 K115 Y116 T118 K119 K120
BS02	MG	1l	P48 N49	P44 N45

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:0015935 small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5vp2, PDBe:5vp2, PDBj:5vp2
• PDBsum: 5vp2
• PubMed: 28505372
• UniProt: Q5SHN3|RS12_THET8 Small ribosomal subunit protein uS12 (Gene Name=rpsL)