Structure of PDB 6xqd Chain 1P

Receptor sequence

>6xqd1P (length=149) Species: 300852 (Thermus thermophilus HB8)

MKLSDLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRR
FEGGRSTTLMRLPKRGMQGQVPGEIKRPRYQGVNLKDLARFEGEVTPELL
VRAGLLKKGYRLKILGEGEAKPLKVVAHAFSKSALEKLKAAGGEPVLLE

3D structure

• PDB: 6xqd Sarecycline interferes with tRNA accommodation and tethers mRNA to the 70S ribosome.
• Chain: 1P
• 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	1P	L3 S4 R7 P8 N9 A12 N13 K14 R16 K17 R18 G20 R21 G22 P23 G24 S25 G28 K29 T30 A31 T32 R33 G34 H35 K36 G37 Q38 K39 S40 R41 S42 G43 L45 K46 P48 R50 F51 E52 G53 G54 R55 S56 M60 R61 L62 P63 K64 R65 G66 M67 G69 Q70 V71 P72 G73 E74 I75 K76 R77 Q81 N84 R90 G104 L105 K107 K108 K113 L115 G116 E117 S131 K132 S133	L3 S4 R7 P8 N9 A12 N13 K14 R16 K17 R18 G20 R21 G22 P23 G24 S25 G28 K29 T30 A31 T32 R33 G34 H35 K36 G37 Q38 K39 S40 R41 S42 G43 L45 K46 P48 R50 F51 E52 G53 G54 R55 S56 M60 R61 L62 P63 K64 R65 G66 M67 G69 Q70 V71 P72 G73 E74 I75 K76 R77 Q81 N84 R90 G104 L105 K107 K108 K113 L115 G116 E117 S131 K132 S133
BS02	MG	1P	K36 G37	K36 G37
BS03	MG	1P	G34 H35 K36 S40	G34 H35 K36 S40

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6xqd, PDBe:6xqd, PDBj:6xqd
• PDBsum: 6xqd
• PubMed: 32817463
• UniProt: Q5SHQ7|RL15_THET8 Large ribosomal subunit protein uL15 (Gene Name=rplO)