Structure of PDB 8g9z Chain A Binding Site BS02

Receptor Information
>8g9z Chain A (length=466) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RLVSPAYVRQGCEARRSHEHLIRLLLEKGKCPENGWDESTLELFLHELAI
MDSNNFLGNCGVGEREGRVASALVARRHYRFIHGIGRAVQPKAAGSSLLN
KITNSLVLDIIKLAGVHTVANCFVVPMATGMSLTLCFLTLRHKRPKAKYI
IWPRIDQKSCFKSMITAGFEPVVIENVLEGDELRTDLKAVEAKVQELGPD
CILCIHSTTSCFAPRVPDRLEELAVICANYDIPHIVNNAYGVQSSKCMHL
IQQGARVGRIDAFVQSLDKNFMVPVGGAIIAGFNDSFIQEISKMYPGRAS
ASPSLDVLITLLSLGSNGYKKLLKERKEMFSYLSNQIKKLSEAYNERLLH
TPHNPISLAMTLKTLDEHRDKAVTQLGSMLFTRQVSGARVVPLGSMQTVS
GYTFRGFMSHTNNYPCAYLNAASAIGMKMQDVDLFIKRLDRCLKAVRKER
SKDVDIEEMALKLDNA
Ligand information
Ligand IDPLR
InChIInChI=1S/C8H12NO5P/c1-5-7(4-14-15(11,12)13)3-9-6(2)8(5)10/h3,10H,4H2,1-2H3,(H2,11,12,13)
InChIKeyRBCOYOYDYNXAFA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C)c1O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C)C
OpenEye OEToolkits 1.5.0Cc1c(cnc(c1O)C)COP(=O)(O)O
FormulaC8 H12 N O5 P
Name(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE;
4'-DEOXYPYRIDOXINE PHOSPHATE
ChEMBLCHEMBL1235333
DrugBank
ZINCZINC000001656021
PDB chain8g9z Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8g9z Structural basis for the tRNA-dependent activation of the terminal complex of selenocysteine synthesis in humans.
Resolution2.07 Å
Binding residue
(original residue number in PDB)		A143 T144 G145 Q172 S174 C175 N252 A254 Y255 K284
Binding residue
(residue number reindexed from 1)		A128 T129 G130 Q157 S159 C160 N237 A239 Y240 K269
Annotation score1
Enzymatic activity
Enzyme Commision number 2.9.1.2: O-phospho-L-seryl-tRNA(Sec):L-selenocysteinyl-tRNA synthase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0098621 O-phosphoseryl-tRNA(Sec) selenium transferase activity
Biological Process
GO:0001514 selenocysteine incorporation
GO:0001717 conversion of seryl-tRNAsec to selenocys-tRNAsec
GO:0006412 translation
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8g9z, PDBe:8g9z, PDBj:8g9z
PDBsum8g9z
PubMed36929010
UniProtQ9HD40|SPCS_HUMAN O-phosphoseryl-tRNA(Sec) selenium transferase (Gene Name=SEPSECS)

[Back to BioLiP]