Structure of PDB 1ls3 Chain D Binding Site BS01

Receptor Information
>1ls3 Chain D (length=456) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALG
SCLNNKYSEGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQ
PYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIF
FESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRLRK
IADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRAGM
IFYRRGVYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMTPEFKEYQ
RQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLE
ACSIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRG
IELTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEVESFAALFPL
PGLPGF
Ligand information
Ligand IDPLP
InChIInChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
InChIKeyNGVDGCNFYWLIFO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C=O)C
FormulaC8 H10 N O6 P
NamePYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate
ChEMBLCHEMBL82202
DrugBankDB00114
ZINCZINC000001532514
PDB chain1ls3 Chain C Residue 419A [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ls3 Location of the Pteroylpolyglutamate Binding Site on Rabbit Cytosolic Serine Hydroxymethyltransferase
Resolution2.7 Å
Binding residue
(original residue number in PDB)		Y55 G262 G263
Binding residue
(residue number reindexed from 1)		Y57 G274 G275
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y55 E57 D200 T226 K229 R235
Catalytic site (residue number reindexed from 1) Y57 E59 D212 T238 K241 R247
Enzyme Commision number 2.1.2.1: glycine hydroxymethyltransferase.
Gene Ontology
Molecular Function
GO:0000900 mRNA regulatory element binding translation repressor activity
GO:0004372 glycine hydroxymethyltransferase activity
GO:0008270 zinc ion binding
GO:0016740 transferase activity
GO:0030170 pyridoxal phosphate binding
GO:0036094 small molecule binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0048027 mRNA 5'-UTR binding
GO:0050897 cobalt ion binding
GO:0070905 serine binding
Biological Process
GO:0006544 glycine metabolic process
GO:0006563 L-serine metabolic process
GO:0006565 L-serine catabolic process
GO:0006730 one-carbon metabolic process
GO:0009113 purine nucleobase biosynthetic process
GO:0017148 negative regulation of translation
GO:0019264 glycine biosynthetic process from serine
GO:0035999 tetrahydrofolate interconversion
GO:0046653 tetrahydrofolate metabolic process
GO:0046655 folic acid metabolic process
GO:0051289 protein homotetramerization
GO:1904482 cellular response to tetrahydrofolate
GO:1990830 cellular response to leukemia inhibitory factor
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
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:1ls3, PDBe:1ls3, PDBj:1ls3
PDBsum1ls3
PubMed12438316
UniProtP07511|GLYC_RABIT Serine hydroxymethyltransferase, cytosolic (Gene Name=SHMT1)

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