Structure of PDB 1pyg Chain A Binding Site BS02

Receptor Information
>1pyg Chain A (length=801) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKQISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTV
RDHLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACD
EATYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGI
RYEFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHT
SQGAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPQAVLDRNLAE
NISKELRLKQEYFVVAATLQDIIRRFKSSKFGCRDPVRTNFDAFPDKVAI
QLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVLPEALE
RWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSLVEEGA
VKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQNKTNG
ITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAFIRDVA
KVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNCLHVIT
LYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDVVNHDPV
VGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNMKFMLNG
ALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQEYYDRI
PELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEYVKCQE
RVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSRQRLP
A
Ligand information
Ligand IDPDP
InChIInChI=1S/C8H11NO9P2/c1-5-8(11)7(3-10)6(2-9-5)4-17-20(15,16)18-19(12,13)14/h2-3,11H,4H2,1H3,(H,15,16)(H2,12,13,14)
InChIKeyBLPOUZDLIYAHLN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)OP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCc1cnc(c(O)c1C=O)C
CACTVS 3.341Cc1ncc(CO[P](O)(=O)O[P](O)(O)=O)c(C=O)c1O
CACTVS 3.341Cc1ncc(CO[P@@](O)(=O)O[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)CO[P@](=O)(O)OP(=O)(O)O)C=O)O
FormulaC8 H11 N O9 P2
NamePYRIDOXAL-5'-DIPHOSPHATE
ChEMBL
DrugBank
ZINC
PDB chain1pyg Chain A 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]
PDB1pyg Structural basis for the activation of glycogen phosphorylase b by adenosine monophosphate.
Resolution2.87 Å
Binding residue
(original residue number in PDB)		Y90 K568 R649 G675 T676 G677 K680
Binding residue
(residue number reindexed from 1)		Y81 K533 R614 G640 T641 G642 K645
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H342 K533 R534 K539 T641 K645
Enzyme Commision number 2.4.1.1: glycogen phosphorylase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004645 1,4-alpha-oligoglucan phosphorylase activity
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
GO:0098723 skeletal muscle myofibril

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1pyg, PDBe:1pyg, PDBj:1pyg
PDBsum1pyg
PubMed1962195
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

[Back to BioLiP]