Structure of PDB 1ygp Chain B Binding Site BS03

Receptor Information
>1ygp Chain B (length=858) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TRRLTGFLPQEIKSIDTMIPLLSRALWNKHQVKKFNKAEDFQDRFIDHVE
TTLARSLYNCDDMVAYEAASMSIRDNLVIDWNKTQQKFTTRDPKRVYYLS
LEFLMGRALDNALINMKIPREMIKGALDELGFKLEDVLDQEPDAGLGNGG
LGRLAACFVDSMATEGIPAWGYGLRYEYGIFAQKIIDGYQVETPDYWLNS
GNPWEIERNEVQIPVTFYGYVDRPTTLSASQWIGGERVLAVAYDFPVPGF
KTSNVNNLRLWQARPTTEFDLNKFNNGDYKNSVAQQQRAESITAVLYPND
NFAQGKELRLKQQYFWCAASLHDILRRFKKSKRPWTEFPDQVAIQLNDTH
PTLAIVELQRVLVDLEKLDWHEAWDIVTKTFAYTNHTVMQEALEKWPRRL
FGHLLPRHLEIIYDINWFFLEDVAKKFPKDVDLLSRISIIEENSPERQIR
MAFLAIVGSHKVNGVVELHSELIKTTIFKDFIKFYGPSKFVNVTNGITPR
RWLKQANPSLAKLISETLNDPTEEYLLDMAKLTQLEKYVEDKEFLKKWNQ
VKLNNKIRLVDLIKKENDGVDIINREYLDDTLFDMQVKRIHEYKRQQLNV
FGIIYRYLAMKNMLKNGASIEEVARKYPRKVSIFGGKSAPGYYMAKLIIK
LINCVADIVNNDESIEHLLKVVFVADYNVSKAEIIIPASDLSEHISTAGT
EASGTSNMKFVMNGGLIIGTVDGANVEITREIGEDNVFLFGNLSENVEEL
RYNHQYHPQDLPSSLDSVLSYIEQFSPENPNEFKPLVDSIKYHGDYYLVS
DDFESYLATHELVDQEFHNQRSEWLKKSVLSLANVGFFSSDRCIEEYSDT
IWNVEPVT
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 chain1ygp Chain B Residue 860 [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]
PDB1ygp A protein phosphorylation switch at the conserved allosteric site in GP.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		L90 G135 R138 W491 N649 V650 S677 K680
Binding residue
(residue number reindexed from 1)		L104 G150 R153 W502 N678 V679 S706 K709
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H386 K588 R589 K594 T705 K709
Enzyme Commision number 2.4.1.1: glycogen phosphorylase.
Gene Ontology
Molecular Function
GO:0004645 1,4-alpha-oligoglucan phosphorylase activity
GO:0005515 protein binding
GO:0008184 glycogen phosphorylase activity
GO:0016757 glycosyltransferase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0005977 glycogen metabolic process
GO:0005980 glycogen catabolic process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1ygp, PDBe:1ygp, PDBj:1ygp
PDBsum1ygp
PubMed8703213
UniProtP06738|PHSG_YEAST Glycogen phosphorylase (Gene Name=GPH1)

[Back to BioLiP]