Structure of PDB 1em6 Chain B

Receptor sequence
>1em6B (length=787) Species: 9606 (Homo sapiens) [Search protein sequence]
ENVAELKKSFNRHLHFTLVKDRNVATTRDYYFALAHTVRDHLVGRWIRTQ
QHYYDKCPKRVYYLSLEFYMGRTLQNTMINLGLQNACDEAIYQLGLDIEE
LEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEYGIFNQKIR
DGWQVEEADDWLRYGNPWEKSRPEFMLPVHFYGKVEHTNTGTKWIDTQVV
LALPYDTPVPGYMNNTVNTMRLWSARAPGDYIQAVLDRNLAENISRVLYP
NDNFFEGKELRLKQEYFVVAATLQDIIRRFKASTVFDAFPDQVAIQLNDT
HPALAIPELMRIFVDIEKLPWSKAWELTQKTFAYTNHTVLPEALERWPVD
LVEKLLPRHLEIIYEINQKHLDRIVALFPKDVDRLRRMSLIEEEGSKRIN
MAHLCIVGSHAVNGVAKIHSDIVKTKVFKDFSELEPDKFQNKTNGITPRR
WLLLCNPGLAELIAEKIGEDYVKDLSQLTKLHSFLGDDVFLRELAKVKQE
NKLKFSQFLETEYKVKINPSSMFDVQVKRIHEYKRQLLNCLHVITMYNRI
KKDPFVPRTVIIGGKAAPGYHMAKMIIKLITSVADVVNNDPMVGSKLKVI
FLENYRVSLAEKVIPATDLSEQISTAGTEASGTGNMKFMLNGALTIGTMD
GANVEMAEEAGEENLFIFGMRIDDVAALDKKGYEAKEYYEALPELKLVID
QIDNGFFSPKQPDLFKDIINMLFYHDRFKVFADYEAYVKCQDKVSQLYMN
PKAWNTMVLKNIAASGKFSSDRTIKEYAQNIWNVEPS
3D structure
PDB1em6 Human liver glycogen phosphorylase inhibitors bind at a new allosteric site.
ChainB
Resolution2.2 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) H337 K528 R529 K534 T633 K637
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 CP4 B T38 V40 R60 W67 E190 K191 P229 T17 V19 R39 W46 E169 K170 P208 PDBbind-CN: -logKd/Ki=8.22,IC50=6nM
BindingDB: IC50=6.0nM
BS02 NBG B L136 L139 N284 H377 V455 N484 E672 S674 G675 L115 L118 N253 H337 V415 N444 E629 S631 G632
BS03 PLP B Y90 G135 W491 K568 Y648 R649 V650 G675 T676 G677 K680 Y69 G114 W451 K528 Y605 R606 V607 G632 T633 G634 K637
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1em6, PDBe:1em6, PDBj:1em6
PDBsum1em6
PubMed10980448
UniProtP06737|PYGL_HUMAN Glycogen phosphorylase, liver form (Gene Name=PYGL)

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