Structure of PDB 3ddw Chain A

Receptor sequence

>3ddwA (length=811) Species: 9606 (Homo sapiens) [Search protein sequence]

QISIRGIVGVENVAELKKSFNRHLHFTLVKDRNVATTRDYYFALAHTVRD
HLVGRWIRTQQHYYDKCPKRVYYLSLEFYMGRTLQNTMINLGLQNACDEA
IYQLGLDIEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRY
EYGIFNQKIRDGWQVEEADDWLRYGNPWEKSRPEFMLPVHFYGKVEHTNT
GTKWIDTQVVLALPYDTPVPGYMNNTVNTMRLWSARAPNDGDYIQAVLDR
NLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKASKFGST
RGAGTVFDAFPDQVAIQLNDTHPALAIPELMRIFVDIEKLPWSKAWELTQ
KTFAYTNHTVLPEALERWPVDLVEKLLPRHLEIIYEINQKHLDRIVALFP
KDVDRLRRMSLIEEEGSKRINMAHLCIVGSHAVNGVAKIHSDIVKTKVFK
DFSELEPDKFQNKTNGITPRRWLLLCNPGLAELIAEKIGEDYVKDLSQLT
KLHSFLGDDVFLRELAKVKQENKLKFSQFLETEYKVKINPSSMFDVQVKR
IHEYKRQLLNCLHVITMYNRIKKDPKKLFVPRTVIIGGKAAPGYHMAKMI
IKLITSVADVVNNDPMVGSKLKVIFLENYRVSLAEKVIPATDLSEQISTA
GTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENLFIFGMRIDDVA
ALDKKGYEAKEYYEALPELKLVIDQIDNGFFSPKQPDLFKDIINMLFYHD
RFKVFADYEAYVKCQDKVSQLYMNPKAWNTMVLKNIAASGKFSSDRTIKE
YAQNIWNVEPS

3D structure

PDB

3ddw 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.

Chain

Resolution

1.9 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)	H358 K549 R550 K555 T657 K661
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	NBG	A	L136 N284 H377 V455 N484 E672 S674 G675	L125 N265 H358 V436 N465 E653 S655 G656
BS02	PLP	A	Y90 G134 G135 K568 Y648 R649 V650 G675 T676 G677 K680	Y79 G123 G124 K549 Y629 R630 V631 G656 T657 G658 K661
BS03	CFF	A	F285 H571 A610 G612 Y613	F266 H552 A591 G593 Y594
BS04	055	A	W67 Q71 Q72 R193 R310	W56 Q60 Q61 R182 R291	MOAD: ic50=1067nM
BS05	055	A	V40 K41 D42 V45	V29 K30 D31 V34	MOAD: ic50=1067nM

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:3ddw, PDBe:3ddw, PDBj:3ddw
PDBsum	3ddw
PubMed	19138846
UniProt	P06737\|PYGL_HUMAN Glycogen phosphorylase, liver form (Gene Name=PYGL)

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