Structure of PDB 5vp2 Chain 10

Receptor sequence

>5vp210 (length=83) Species: 300852 (Thermus thermophilus HB8)

AHKKGLGSTRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNV
GMGRDFTLFALVDGVVEFQDRGRLGRYVHVRPL

3D structure

• PDB: 5vp2 Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state.
• Chain: 10
• 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	10	A2 H3 K4 S9 T10 N12 R14 D15 S16 Q17 A18 K19 R20 K24 Y26 E27 Q29 A33 G34 N35 I36 R39 R41 G42 T43 G54 R55 D56 F57 T58 F60 F69 R74 L75 R77	A1 H2 K3 S8 T9 N11 R13 D14 S15 Q16 A17 K18 R19 K23 Y25 E26 Q28 A32 G33 N34 I35 R38 R40 G41 T42 G53 R54 D55 F56 T57 F59 F68 R73 L74 R76
BS02	rna	10	R72 R74	R71 R73
BS03	rna	10	G8 R11	G7 R10
BS04	MG	10	G22 V23	G21 V22
BS05	MG	10	S9 T10 R11	S8 T9 R10
BS06	MG	10	Q17 A18	Q16 A17

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: P60493|RL27_THET8 Large ribosomal subunit protein bL27 (Gene Name=rpmA)