Structure of PDB 6y6x Chain LS

Receptor sequence

>6y6xLS (length=175) Species: 9606 (Homo sapiens)

KASGTLREYKVVGRCLPTPKCHTPPLYRMRIFAPNHVVAKSRFWYFVSQL
KKMKKSSGEIVYCGQVFEKSPLRVKNFGIWLRYDSRSGTHNMYREYRDLT
TAGAVTQCYRDMGARHRARAHSIQIMKVEEIAASKCRRPAVKQFHDSKIK
FPLPHRVLRRQHKPRFTTKRPNTFF

3D structure

• PDB: 6y6x Tetracenomycin X inhibits translation by binding within the ribosomal exit tunnel.
• Chain: LS
• 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	LS	S4 G5 R8 Y63 Q66 V67 F68 K70 P72 S86 R87 S88 H91 N92 M93 Y94 R95 R98 R111 G114 A115 R116 H117 R118 R120 A134 R139 H146 D147 S148 K149 P155 H156 R157 V158 R160 R161 H163 K164 P165 R166 T168 T169 K170 R171 P172 N173 T174 F175 F176	S3 G4 R7 Y62 Q65 V66 F67 K69 P71 S85 R86 S87 H90 N91 M92 Y93 R94 R97 R110 G113 A114 R115 H116 R117 R119 A133 R138 H145 D146 S147 K148 P154 H155 R156 V157 R159 R160 H162 K163 P164 R165 T167 T168 K169 R170 P171 N172 T173 F174 F175
BS02	rna	LS	S42 R43 Y46 S49 K53 K55 K56 S57 R87 R120 H122	S41 R42 Y45 S48 K52 K54 K55 S56 R86 R119 H121

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6y6x, PDBe:6y6x, PDBj:6y6x
• PDBsum: 6y6x
• PubMed: 32601485
• UniProt: Q02543|RL18A_HUMAN Large ribosomal subunit protein eL20 (Gene Name=RPL18A)