Structure of PDB 3gpb Chain A Binding Site BS03

Receptor Information
>3gpb Chain A (length=833) 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
SQGAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNV
GGYIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIR
RFKSSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERL
DWDKAWEVTVKTCAYTNHTVIPEALERWPVHLLETLLPRHLQIIYEINQR
FLNRVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIH
SEILKKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGE
EYISDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINP
NSLFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKA
APGYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPA
ADLSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFF
IFGMRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFK
DIVNMLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSG
KFSSDRTIAQYAREIWGVEPSRQRLPAPDEKIP
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 chain3gpb Chain A Residue 999 [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]
PDB3gpb Comparison of the binding of glucose and glucose 1-phosphate derivatives to T-state glycogen phosphorylase b.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		G134 W491 K568 Y648 R649 G675 G677 K680
Binding residue
(residue number reindexed from 1)		G125 W482 K559 Y639 R640 G666 G668 K671
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H368 K559 R560 K565 T667 K671
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:3gpb, PDBe:3gpb, PDBj:3gpb
PDBsum3gpb
PubMed2125493
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

[Back to BioLiP]