Structure of PDB 1l5s Chain B

Receptor sequence
>1l5sB (length=791) Species: 9606 (Homo sapiens) [Search protein sequence]
NVAELKKSFNRHLHFTLVKDRNVATTRDYYFALAHTVRDHLVGRWIRTQQ
HYYDKCPKRVYYLSLEFYMGRTLQNTMINLGLQNACDEAIYQLGLDIEEL
EEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEYGIFNQKIRD
GWQVEEADDWLRYGNPWEKSRPEFMLPVHFYGKVEHTNTGTKWIDTQVVL
ALPYDTPVPGYMNNTVNTMRLWSARAPNDDYIQAVLDRNLAENISRVLYP
NDNFFEGKELRLKQEYFVVAATLQDIIRRFKASKFVFDAFPDQVAIQLND
THPALAIPELMRIFVDIEKLPWSKAWELTQKTFAYTNHTVLPEALERWPV
DLVEKLLPRHLEIIYEINQKHLDRIVALFPKDVDRLRRMSLIEEEGSKRI
NMAHLCIVGSHAVNGVAKIHSDIVKTKVFKDFSELEPDKFQNKTNGITPR
RWLLLCNPGLAELIAEKIGEDYVKDLSQLTKLHSFLGDDVFLRELAKVKQ
ENKLKFSQFLETEYKVKINPSSMFDVQVKRIHEYKRQLLNCLHVITMYNR
IKKDPKKLFVPRTVIIGGKAAPGYHMAKMIIKLITSVADVVNNDPMVGSK
LKVIFLENYRVSLAEKVIPATDLSEQISTAGTEASGTGNMKFMLNGALTI
GTMDGANVEMAEEAGEENLFIFGMRIDDVAALDKKGYEAKEYYEALPELK
LVIDQIDNGFFSPKQPDLFKDIINMLFYHDRFKVFADYEAYVKCQDKVSQ
LYMNPKAWNTMVLKNIAASGKFSSDRTIKEYAQNIWNVEPS
3D structure
PDB1l5s Structure-activity analysis of the purine binding site of human liver glycogen phosphorylase.
ChainB
Resolution2.1 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H338 K529 R530 K535 T637 K641
Enzyme Commision number 2.4.1.1: glycogen phosphorylase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 700 B T38 V40 F53 H57 Y185 P188 T16 V18 F31 H35 Y163 P166 MOAD: ic50=0.145uM
BindingDB: IC50=45nM
BS02 NBG B L136 N284 H377 T378 V455 N484 E672 S674 G675 L114 N253 H338 T339 V416 N445 E633 S635 G636
BS03 PLP B Y90 G135 K568 Y648 R649 G675 T676 G677 K680 Y68 G113 K529 Y609 R610 G636 T637 G638 K641
BS04 700 B R60 W67 P188 E190 K191 R38 W45 P166 E168 K169 MOAD: ic50=0.145uM
BindingDB: IC50=45nM
BS05 URC B N282 F285 A610 G612 Y613 N251 F254 A571 G573 Y574 MOAD: Kd=550uM
PDBbind-CN: -logKd/Ki=3.26,Kd=550uM
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0002060 purine nucleobase binding
GO:0004645 1,4-alpha-oligoglucan phosphorylase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0005536 D-glucose binding
GO:0008184 glycogen phosphorylase activity
GO:0016208 AMP binding
GO:0016757 glycosyltransferase activity
GO:0019842 vitamin binding
GO:0030170 pyridoxal phosphate binding
GO:0030246 carbohydrate binding
GO:0032052 bile acid binding
GO:0042802 identical protein binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0005977 glycogen metabolic process
GO:0005980 glycogen catabolic process
GO:0006015 5-phosphoribose 1-diphosphate biosynthetic process
GO:0009617 response to bacterium
GO:0042593 glucose homeostasis
GO:0070266 necroptotic process
Cellular Component
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0034774 secretory granule lumen
GO:0070062 extracellular exosome
GO:1904813 ficolin-1-rich granule lumen

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1l5s, PDBe:1l5s, PDBj:1l5s
PDBsum1l5s
PubMed12204691
UniProtP06737|PYGL_HUMAN Glycogen phosphorylase, liver form (Gene Name=PYGL)

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