Structure of PDB 5f8k Chain 1D

Receptor sequence

>5f8k1D (length=275) Species: 300852 (Thermus thermophilus HB8)

AVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITV
RFRGGGHKRLYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGE
KRYIIAPDGLQVGQQVVAGPDAPIQVGNALPLRFIPVGTVVHAVELEPKK
GAKLARAAGTSAQIQGREGDYVILRLPSGELRKVHGECYATVGAVGNADH
KNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAPRGRPPASPWG
WQTKGLKTRKRRKPSSRFIIARRKK

3D structure

• PDB: 5f8k Structure of the mammalian antimicrobial peptide Bac7(1-16) bound within the exit tunnel of a bacterial ribosome.
• Chain: 1D
• 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	1D	K7 P8 Y9 T10 S12 R13 R14 F15 K35 K39 T40 G42 R43 N44 N45 Q46 R48 I49 T50 V51 R52 R54 G56 H58 K59 R60 L61 Y62 R63 Y84 P86 N87 R88 D99 G100 E101 K102 L147 E148 K151 K154 L155 A156 R157 A158 A159 G160 Y172 P178 S179 E181 R183 A199 H201 K202 V205 L206 G207 K208 A209 G210 R211 S212 R213 W214 R218 P219 H220 V221 R222 G223 A224 A225 M226 N227 P228 V229 D230 H231 H233 G236 E237 G238 R239 P241 R242 G243 R244 P246 A247 S248 P249 W250 W252 Q253 T254 K255 G256 L257 K258 T259 R260 K261 R263 K264 S266 R268 F269 R273 R274	K6 P7 Y8 T9 S11 R12 R13 F14 K34 K38 T39 G41 R42 N43 N44 Q45 R47 I48 T49 V50 R51 R53 G55 H57 K58 R59 L60 Y61 R62 Y83 P85 N86 R87 D98 G99 E100 K101 L146 E147 K150 K153 L154 A155 R156 A157 A158 G159 Y171 P177 S178 E180 R182 A198 H200 K201 V204 L205 G206 K207 A208 G209 R210 S211 R212 W213 R217 P218 H219 V220 R221 G222 A223 A224 M225 N226 P227 V228 D229 H230 H232 G235 E236 G237 R238 P240 R241 G242 R243 P245 A246 S247 P248 W249 W251 Q252 T253 K254 G255 L256 K257 T258 R259 K260 R262 K263 S265 R267 F268 R272 R273
BS02	MG	1D	H220 R222	H219 R221
BS03	MG	1D	P241 R242	P240 R241
BS04	MG	1D	K5 F6 R14	K4 F5 R13
BS05	MG	1D	D85 A90 R91	D84 A89 R90
BS06	MG	1D	G235 G236	G234 G235
BS07	MG	1D	R52 F53 R54	R51 F52 R53

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5f8k, PDBe:5f8k, PDBj:5f8k
• PDBsum: 5f8k
• PubMed: 26792896
• UniProt: P60405|RL2_THET8 Large ribosomal subunit protein uL2 (Gene Name=rplB)