Structure of PDB 5vp2 Chain 18

Receptor sequence

>5vp218 (length=64) Species: 300852 (Thermus thermophilus HB8)

PKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLA
KPEAERIKLLLPYE

3D structure

• PDB: 5vp2 Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state.
• Chain: 18
• 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	18	P2 K3 M4 K5 T6 K8 K12 R13 K15 T17 A18 S19 K26 T27 G28 K29 R30 H31 L32 N33 W34 Q35 K39 I41 R42 Q43 K44 R46 K47 A51 K52 P53 Y64	P1 K2 M3 K4 T5 K7 K11 R12 K14 T16 A17 S18 K25 T26 G27 K28 R29 H30 L31 N32 W33 Q34 K38 I40 R41 Q42 K43 R45 K46 A50 K51 P52 Y63
BS02	MG	18	L32 W34	L31 W33
BS03	MG	18	S37 G38	S36 G37
BS04	MG	18	K59 L62	K58 L61

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5vp2, PDBe:5vp2, PDBj:5vp2
• PDBsum: 5vp2
• PubMed: 28505372
• UniProt: Q5SKU1|RL35_THET8 Large ribosomal subunit protein bL35 (Gene Name=rpmI)