Structure of PDB 8gpb Chain A Binding Site BS03

Receptor Information
>8gpb Chain A (length=832) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KQISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVR
DHLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDE
ATYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIR
YEFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTS
QGAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNVG
GYIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRR
FKSSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLD
WDKAWEVTVKTCAYTNHTVIPEALERWPVHLLETLLPRHLQIIYEINQRF
LNRVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHS
EILKKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEE
YISDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPN
SLFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAA
PGYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAA
DLSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFI
FGMRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKD
IVNMLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGK
FSSDRTIAQYAREIWGVEPSRQRLPAPDEKIP
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain8gpb Chain A Residue 940 [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]
PDB8gpb Structural mechanism for glycogen phosphorylase control by phosphorylation and AMP.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		N282 F285 P611 G612 Y613
Binding residue
(residue number reindexed from 1)		N272 F275 P601 G602 Y603
Annotation score1
Binding affinityMOAD: Kd=250uM
PDBbind-CN: -logKd/Ki=3.60,Kd=0.25mM
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H367 K558 R559 K564 T666 K670
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:8gpb, PDBe:8gpb, PDBj:8gpb
PDBsum8gpb
PubMed1900534
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

[Back to BioLiP]