Structure of PDB 8xsx Chain CB

Receptor sequence

>8xsxCB (length=846) Species: 9606 (Homo sapiens)

NFTVDQIRAIMDKKANIRNMSVIAHVDHGKSTLTDSLVCKAGIIASARAG
ETRFTDTRKDEQERCITIKSTAISLFYELSENDLNFIKQSKDGAGFLINL
IDSPGHVDFSSEVTAALRVTDGALVVVDCVSGVCVQTETVLRQAIAERIK
PVLMMNKMDRALLELQLEPEELYQTFQRIVENVNVIISTYGEGESGPMGN
IMIDPVLGTVGFGSGLHGWAFTLKQFAEMYVAKFAERAKKVEDMMKKLWG
DRYFDPANGKFSKSATSPEGKKLPRTFCQLILDPIFKVFDAIMNFKKEET
AKLIEKLDIKLDSEDKDKEGKPLLKAVMRRWLPAGDALLQMITIHLPSPV
TAQKYRCELLYEGPPDDEAAMGIKSCDPKGPLMMYISKMVPTSDKGRFYA
FGRVFSGLVSTGLKVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEPIE
DVPCGNIVGLVGVDQFLVKTGTITTFEHAHNMRVMKFSVSPVVRVAVEAK
NPADLPKLVEGLKRLAKSDPMVQCIIEESGEHIIAGAGELHLEICLKDLE
EDHACIPIKKSDPVVSYRETVSEESNVLCLSKSPNKHNRLYMKARPFPDG
LAEDIDKGEVSARQELKQRARYLAEKYEWDVAEARKIWCFGPDGTGPNIL
TDITKGVQYLNEIKDSVVAGFQWATKEGALCEENMRGVRFDVHDVTLHAD
AIHRGGGQIIPTARRCLYASVLTAQPRLMEPIYLVEIQCPEQVVGGIYGV
LNRKRGHVFEESQVAGTPMFVVKAYLPVNESFGFTADLRSNTGGQAFPQC
VFDHWQILPGDPFDNSSRPSQVVAETRKRKGLKEGIPALDNFLDKL

3D structure

• PDB: 8xsx Structural basis for differential inhibition of eukaryotic ribosomes by tigecycline.
• Chain: CB
• Resolution: 2.4 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	CB	H27 H108 V109 R162 P596 Y760 R765 V770 F771 F782 R801 S802 G805 G806	H25 H106 V107 R160 P584 Y748 R753 V758 F759 F770 R789 S790 G793 G794
BS02	rna	CB	D406 R409 R449 N597 K629 R633 K667 G668 V669 H715 Q720	D394 R397 R437 N585 K617 R621 K655 G656 V657 H703 Q708
BS03	ADP	CB	D29 G31 K32 S33 T34 N158 K159 D161 S216 L218	D27 G29 K30 S31 T32 N156 K157 D159 S214 L216

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003746 translation elongation factor activity
• GO:0003924 GTPase activity
• GO:0005515 protein binding
• GO:0005525 GTP binding
• GO:0016787 hydrolase activity
• GO:0019901 protein kinase binding
• GO:0043022 ribosome binding
• GO:0045296 cadherin binding

Biological Process

• GO:0002244 hematopoietic progenitor cell differentiation
• GO:0006412 translation
• GO:0006414 translational elongation
• GO:0045727 positive regulation of translation

Cellular Component

• GO:0005576 extracellular region
• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0016235 aggresome
• GO:0034774 secretory granule lumen
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1904813 ficolin-1-rich granule lumen
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8xsx, PDBe:8xsx, PDBj:8xsx
• PDBsum: 8xsx
• PubMed: 38942792
• UniProt: P13639|EF2_HUMAN Elongation factor 2 (Gene Name=EEF2)