Structure of PDB 1rv3 Chain B Binding Site BS01

Receptor Information
>1rv3 Chain B (length=466) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WSSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEA
LGSCLNNKYSLGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVN
VQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATS
IFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRL
RKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRA
GMIFYRRGVRSVDKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQ
AMTPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGT
DGGRAEKVLEACSIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDF
QKVAHFIHRGIELTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQE
VESFAALFPLPGLPGF
Ligand information
Ligand IDGLY
InChIInChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5)
InChIKeyDHMQDGOQFOQNFH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C(=O)O)N
CACTVS 3.341NCC(O)=O
ACDLabs 10.04O=C(O)CN
FormulaC2 H5 N O2
NameGLYCINE
ChEMBLCHEMBL773
DrugBankDB00145
ZINCZINC000004658552
PDB chain1rv3 Chain B Residue 602 [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]
PDB1rv3 Serine Hydroxymethyltransferase: Role of Glu75 and Evidence that Serine Is Cleaved by a Retroaldol Mechanism.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		S53 H231 K257 R402
Binding residue
(residue number reindexed from 1)		S39 H217 K243 R384
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) Y73 L75 D228 T254 K257 R263
Catalytic site (residue number reindexed from 1) Y59 L61 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:1rv3, PDBe:1rv3, PDBj:1rv3
PDBsum1rv3
PubMed15170323
UniProtP07511|GLYC_RABIT Serine hydroxymethyltransferase, cytosolic (Gene Name=SHMT1)

[Back to BioLiP]