Structure of PDB 4zdl Chain B Binding Site BS01

Receptor Information
>4zdl Chain B (length=444) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RQGCEARRSHEHLIRLLLEKGKCPENGWDESTLELFLHELAIMDSNNFLG
NCGVGEREGRVASALVARRHYRFIHGIGRSGDISAVQPKAAGSSLLNKIT
NSLVLDIIKLAGVHTVANCFVVPMATGMSLTLCFLTLRHKRPKAKYIIWP
RIDQKSCFKSMITAGFEPVVIENVLEGDELRTDLKAVEAKVQELGPDCIL
CIHSTTSCFAPRVPDRLEELAVICANYDIPHIVNNAYGVQSSKCMHLIQQ
GARVGRIDAFVQSLDKNFMVPVGGAIIAGFNDSFIQEISKMYPGRASASP
SLDVLISLLSLGSNGYKKLLKERKEMFSYLSNQIKKLSEAYNERLLHTPH
NPISLAMTLKTLDEHRDKAVTQLGSMLFTRQVSGARVVPLGSMQTVSGYT
FRGFMSHTNNYPCAYLNAASAIGMKMQDVDLFIKRLDRCLKAVR
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 chain4zdl Chain B Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4zdl Structural basis for early-onset neurological disorders caused by mutations in human selenocysteine synthase.
Resolution2.26 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)		A125 T126 G127 Q154 S156 C157 N234 A236 Y237 K266
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R75 R97 S98 Q105 Q172 A254 K284 R313
Catalytic site (residue number reindexed from 1) R57 R79 S80 Q87 Q154 A236 K266 R295
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4zdl, PDBe:4zdl, PDBj:4zdl
PDBsum4zdl
PubMed27576344
UniProtQ9HD40|SPCS_HUMAN O-phosphoseryl-tRNA(Sec) selenium transferase (Gene Name=SEPSECS)

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