Structure of PDB 6yve Chain AAA Binding Site BS01

Receptor Information
>6yve Chain AAA (length=811) 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
GAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFVGGYIQAVL
DRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSKFN
FDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYT
NHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRL
RRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELE
PHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYV
DDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKR
QLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITA
IGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASG
TGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRG
YNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFA
DYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIW
GVEPSRQRLPA
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 chain6yve Chain AAA Residue 901 [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]
PDB6yve Affinity Crystallography Reveals Binding of Pomegranate Juice Anthocyanins at the Inhibitor Site of Glycogen Phosphorylase: The Contribution of a Sugar Moiety to Potency and Its Implications to the Binding Mode.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Y90 G134 K568 Y648 R649 G675 T676 G677 K680
Binding residue
(residue number reindexed from 1)		Y79 G123 K543 Y623 R624 G650 T651 G652 K655
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H352 K543 R544 K549 T651 K655
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:6yve, PDBe:6yve, PDBj:6yve
PDBsum6yve
PubMed32840370
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

[Back to BioLiP]