Structure of PDB 2gpb Chain A Binding Site BS02

Receptor Information
>2gpb Chain A (length=831) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRD
HLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEA
TYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRY
EFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQ
GAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNVGG
YIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRF
KSSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDW
DKAWEVTVKTCAYTNHTVIPEALERWPVHLLETLLPRHLQIIYEINQRFL
NRVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSE
ILKKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEY
ISDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNS
LFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAP
GYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAAD
LSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIF
GMRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDI
VNMLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKF
SSDRTIAQYAREIWGVEPSRQRLPAPDEKIP
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 chain2gpb Chain A Residue 999 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2gpb 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 K568 K574 Y648 R649 V650 G675 T676 G677 K680
Binding residue
(residue number reindexed from 1)		G123 K557 K563 Y637 R638 V639 G664 T665 G666 K669
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H366 K557 R558 K563 T665 K669
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2gpb, PDBe:2gpb, PDBj:2gpb
PDBsum2gpb
PubMed2125493
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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