Structure of PDB 4d5l Chain E

Receptor sequence

>4d5lE (length=257) Species: 9986 (Oryctolagus cuniculus)

ARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIVFLRNR
LKYALTGDEVKKICMQRFIKIDGKVRVDVTYPAGFMDVISIEKTGEHFRL
VYDTKGRFAVHRITVEEAKYKLCKVRKITVGVKGIPHLVTHDARTIRYPD
PVIKVNDTVQIDLGTGKIINFIKFDTGNLCMVIGGANLGRVGVITNRERH
PGSFDVVHVKDANGNSFATRLSNIFVIGNGNKPWISLPRGKGIRLTVAEE
RDKRLAT

3D structure

• PDB: 4d5l Cryo-Em of Ribosomal 80S Complexes with Termination Factors Reveals the Translocated Cricket Paralysis Virus Ires.
• Chain: E
• Resolution: 9.0 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	E	A2 R3 P5 K6 K7 H8 K10 R11 V12 A13 K16 M19 D21 K22 L23 F27 A28 P29 R30 T33 G34 H36 K37 L38 R49 R51 T57 G58 D59 K62 M66 R77 K106 R108 R127 K128 V131 V133 K134 G135 I136 P137 A144 R145 T146 R148 Y149 A187 N188 H201 S204 A219 R221 R240 R255	A1 R2 P4 K5 K6 H7 K9 R10 V11 A12 K15 M18 D20 K21 L22 F26 A27 P28 R29 T32 G33 H35 K36 L37 R48 R50 T56 G57 D58 K61 M65 R76 K105 R107 R126 K127 V130 V132 K133 G134 I135 P136 A143 R144 T145 R147 Y148 A186 N187 H200 S203 A218 R220 R239 R254

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4d5l, PDBe:4d5l, PDBj:4d5l
• PDBsum: 4d5l
• PubMed: 25601755
• UniProt: G1TK17|RS4X_RABIT Small ribosomal subunit protein eS4 (Gene Name=RPS4X)