Structure of PDB 3dd1 Chain B

Receptor sequence
>3dd1B (length=805) Species: 9606 (Homo sapiens) [Search protein sequence]
NVAELKKSFNRHLHFTLVKDRNVATTRDYYFALAHTVRDHLVGRWIRTQQ
HYYDKCPKRVYYLSLEFYMGRTLQNTMINLGLQNACDEAIYQLGLDIEEL
EEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEYGIFNQKIRD
GWQVEEADDWLRYGNPWEKSRPEFMLPVHFYGKVEHTNTGTKWIDTQVVL
ALPYDTPVPGYMNNTVNTMRLWSARAPNDFNLRDFNVGDYIQAVLDRNLA
ENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKASKFGSTGTV
FDAFPDQVAIQLNDTHPALAIPELMRIFVDIEKLPWSKAWELTQKTFAYT
NHTVLPEALERWPVDLVEKLLPRHLEIIYEINQKHLDRIVALFPKDVDRL
RRMSLIEEEGSKRINMAHLCIVGSHAVNGVAKIHSDIVKTKVFKDFSELE
PDKFQNKTNGITPRRWLLLCNPGLAELIAEKIGEDYVKDLSQLTKLHSFL
GDDVFLRELAKVKQENKLKFSQFLETEYKVKINPSSMFDVQVKRIHEYKR
QLLNCLHVITMYNRIKKDPKKLFVPRTVIIGGKAAPGYHMAKMIIKLITS
VADVVNNDPMVGSKLKVIFLENYRVSLAEKVIPATDLSEQISTAGTEASG
TGNMKFMLNGALTIGTMDGANVEMAEEAGEENLFIFGMRIDDVAALDKKG
YEAKEYYEALPELKLVIDQIDNGFFSPKQPDLFKDIINMLFYHDRFKVFA
DYEAYVKCQDKVSQLYMNPKAWNTMVLKNIAASGKFSSDRTIKEYAQNIW
NVEPS
3D structure
PDB3dd1 Anthranilimide based glycogen phosphorylase inhibitors for the treatment of type 2 diabetes. Part 3: X-ray crystallographic characterization, core and urea optimization and in vivo efficacy.
ChainB
Resolution2.57 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) H352 K543 R544 K549 T651 K655
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 25D B K41 D42 V45 K19 D20 V23 BindingDB: IC50=10nM
BS02 NBG B G135 N284 H377 V455 N484 E672 A673 S674 G675 G113 N262 H352 V430 N459 E647 A648 S649 G650
BS03 PLP B Y90 K568 Y648 R649 V650 G675 K680 Y68 K543 Y623 R624 V625 G650 K655
BS04 CFF B F285 H571 G612 Y613 F263 H546 G587 Y588
BS05 25D B W67 Q71 Q72 R193 F196 D227 T240 R310 A313 W45 Q49 Q50 R171 F174 D205 T218 R288 A291 BindingDB: IC50=10nM
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:3dd1, PDBe:3dd1, PDBj:3dd1
PDBsum3dd1
PubMed19138846
UniProtP06737|PYGL_HUMAN Glycogen phosphorylase, liver form (Gene Name=PYGL)

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