Structure of PDB 5dat Chain q2

Receptor sequence

>5datq2 (length=105) Species: 559292 (Saccharomyces cerevisiae S288C)

VNVPKTRKTYCKGKTCRKHTQHKVTQYKAGKASLFAQGKRRYDRKQSGFG
GQTKPVFHKKAKTTKKVVLRLECVKCKTRAQLTLKRCKHFELGGEKKQKG
QALQF

3D structure

• PDB: 5dat Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome
• Chain: q2
• Resolution: 3.15 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	q2	V2 N3 V4 P5 R8 K9 T10 Y11 K13 K15 K19 H20 Y28 G31 A33 S34 F36 A37 Q38 G39 R41 R42 R45 K46 G49 F50 G52 Q53 T54 K55 P56 V57 F58 K60 A62 K63 T65 K66 K67 R80 Q82 K86 C88 K89 K97 K98	V1 N2 V3 P4 R7 K8 T9 Y10 K12 K14 K18 H19 Y27 G30 A32 S33 F35 A36 Q37 G38 R40 R41 R44 K45 G48 F49 G51 Q52 T53 K54 P55 V56 F57 K59 A61 K62 T64 K65 K66 R79 Q81 K85 C87 K88 K96 K97
BS02	ZN	q2	C12 C17 C77	C11 C16 C76
BS03	OHX	q2	K46 S48 G49 F50	K45 S47 G48 F49

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0046677 response to antibiotic
• GO:0046898 response to cycloheximide

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0044391 ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5dat, PDBe:5dat, PDBj:5dat
• PDBsum: 5dat
• UniProt: P0CX27|RL44A_YEAST Large ribosomal subunit protein eL42A (Gene Name=RPL42A)