Structure of PDB 8xbs Chain B Binding Site BS03

Receptor Information
>8xbs Chain B (length=641) Species: 6239 (Caenorhabditis elegans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSVLVFEISSKMKMIEKKLEANTVHVLRLELDQSFILDLTKVAAEIVDSS
KYSKEDGVILEVTVSNGRDSFLLKLPTVYPNLKLYTDGKLLNPLVEQDFH
FHQNLIVTVQSRLNADIDYRLHVTHLDRAQYDFLKFKTGQTTKTLSNQKL
TFVKPIGFFLNCSEQNISQFHVTLYSEDDICANLITVPANESIYDRSVIS
DKTHNRRVLSFTKRADIFFTETEISMFKSFRIFVFIAPDDSGCSSFNEKK
KISFEFKKLENQSYAVPTALMMIFLTTPCLLFLPIVINIIKNSSLHGQML
QYPVAIILPVLMHTAIEFHKWTTSTMANRDEMCFHNHACARPLGELRAWN
NIITNIGYTLYGAIFIVLSICRRGSHVFGTYECTLLDVTIGVFMVLQSIA
SATYHICPSDVAFQFDTPCIQVICGLLMVRQWFVRHESPSPAYTNILLVG
VVSLNFLISAFSKTSYVRFIIAVIHVIVVGSICLAKERSLGSEKLKTRFF
IMAFSMGNFAAIVMYLTLSAFHLNQIATYCFIINCIMYLMYYGCMKVLHS
ERITSKAKLCGALSLLAWAVAGFFFFQDDTDWTRSAAASRALNKPCLLLG
FFGSHDLWHIFGALAGLFTFIFVSFVDDDLINTRKTSINIF
Ligand information
Ligand IDCLR
InChIInChI=1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1
InChIKeyHVYWMOMLDIMFJA-DPAQBDIFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)O)C)C
CACTVS 3.341CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
ACDLabs 10.04OC4CCC3(C(=CCC2C1C(C(C(C)CCCC(C)C)CC1)(C)CCC23)C4)C
OpenEye OEToolkits 1.5.0CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)O)C)C
CACTVS 3.341CC(C)CCC[CH](C)[CH]1CC[CH]2[CH]3CC=C4C[CH](O)CC[C]4(C)[CH]3CC[C]12C
FormulaC27 H46 O
NameCHOLESTEROL
ChEMBLCHEMBL112570
DrugBankDB04540
ZINCZINC000003875383
PDB chain8xbs Chain B Residue 803 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8xbs Structural basis for double-stranded RNA recognition by SID1.
Resolution2.21 Å
Binding residue
(original residue number in PDB)		L674 C679 G696 S699 L700 F757
Binding residue
(residue number reindexed from 1)		L539 C544 G561 S564 L565 F622
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003725 double-stranded RNA binding
GO:0051033 RNA transmembrane transporter activity
Biological Process
GO:0031047 regulatory ncRNA-mediated gene silencing
GO:0033227 dsRNA transport
GO:0035194 regulatory ncRNA-mediated post-transcriptional gene silencing
GO:0050658 RNA transport
Cellular Component
GO:0005764 lysosome
GO:0005886 plasma membrane
GO:0016020 membrane

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8xbs, PDBe:8xbs, PDBj:8xbs
PDBsum8xbs
PubMed38742627
UniProtQ9GZC8|SID1_CAEEL Systemic RNA interference defective protein 1 (Gene Name=sid-1)

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