Structure of PDB 4zdp Chain D Binding Site BS01

Receptor Information
>4zdp Chain D (length=443) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GCEARRSHEHLIRLLLEKGKCPENGWDESTLELFLHELAIMDSNNFLGNC
GVGEREGRVASALVARRHYRFIHGIGRSGDISAVQPKAAGSSLLNKITNS
LVLDIIKLAGVHTVANCFVVPMATGMSLTLCFLTLRHKRPKAKYIIWPRI
DQKSCFKSMITAGFEPVVIENVLEGDELRTDLKAVEAKVQELGPDCILCI
HSTTSCFAPRVPDRLEELAVICANYDIPHIVNNAYGVQSSKCMHLIQQGA
RVGRIDAFVQSLDKNFMVPVGGAIIAGFNDSFIQEISKMYPGRASASPSL
DVLITLLSLGSNGCKKLLKERKEMFSYLSNQIKKLSEAYNERLLHTPHNP
ISLAMTLKTLDEHRDKAVTQLGSMLFTRQVSGARVVPLGSMQTVSGYTFR
GFMSHTNNYPCAYLNAASAIGMKMQDVDLFIKRLDRCLKAVRK
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 chain4zdp Chain D Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4zdp Structural basis for early-onset neurological disorders caused by mutations in human selenocysteine synthase.
Resolution2.703 Å
Binding residue
(original residue number in PDB)		A143 T144 G145 Q172 S174 C175 A254 Y255 K284
Binding residue
(residue number reindexed from 1)		A123 T124 G125 Q152 S154 C155 A234 Y235 K264
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) R55 R77 S78 Q85 Q152 A234 K264 R293
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
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Biological Process
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Cellular Component
External links
PDB RCSB:4zdp, PDBe:4zdp, PDBj:4zdp
PDBsum4zdp
PubMed27576344
UniProtQ9HD40|SPCS_HUMAN O-phosphoseryl-tRNA(Sec) selenium transferase (Gene Name=SEPSECS)

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