Structure of PDB 1rvy Chain A Binding Site BS01

Receptor Information
>1rvy Chain A (length=463) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WSSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEA
LGSCLNNKYSQGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVN
VQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATS
IFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRL
RKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRA
GMIFYRRGVRSEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMT
PEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTDGG
RAEKVLEACSIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQKV
AHFIHRGIELTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEVES
FAALFPLPGLPGF
Ligand information
Ligand IDPLG
InChIInChI=1S/C10H15N2O7P/c1-6-10(15)8(3-11-4-9(13)14)7(2-12-6)5-19-20(16,17)18/h2,11,15H,3-5H2,1H3,(H,13,14)(H2,16,17,18)
InChIKeyFEVQWBMNLWUBTF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CNCC(O)=O)c1O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1CNCC(=O)O)C
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CNCC(=O)O)O
FormulaC10 H15 N2 O7 P
NameN-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE];
N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE
ChEMBL
DrugBankDB02824
ZINCZINC000002046831
PDB chain1rvy Chain A Residue 500 [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]
PDB1rvy Serine Hydroxymethyltransferase: Role of Glu75 and Evidence that Serine Is Cleaved by a Retroaldol Mechanism.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		S53 S119 G120 S121 H148 S203 D228 A230 H231 T254 H256 K257
Binding residue
(residue number reindexed from 1)		S39 S105 G106 S107 H134 S189 D214 A216 H217 T240 H242 K243
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y73 Q75 D228 T254 K257 R263
Catalytic site (residue number reindexed from 1) Y59 Q61 D214 T240 K243 R249
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1rvy, PDBe:1rvy, PDBj:1rvy
PDBsum1rvy
PubMed15170323
UniProtP07511|GLYC_RABIT Serine hydroxymethyltransferase, cytosolic (Gene Name=SHMT1)

[Back to BioLiP]