Structure of PDB 3cem Chain B

Receptor sequence

>3cemB (length=794) Species: 9606 (Homo sapiens) [Search protein sequence]

NVAELKKSFNRHLHFTLVKDRNVATTRDYYFALAHTVRDHLVGRWIRTQQ
HYYDKCPKRVYYLSLEFYMGRTLQNTMINLGLQNACDEAIYQLGLDIEEL
EEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEYGIFNQKIRD
GWQVEEADDWLRYGNPWEKSRPEFMLPVHFYGKVEHTNTGTKWIDTQVVL
ALPYDTPVPGYMNNTVNTMRLWSARAPNDFDYIQAVLDRNLAENISRVLY
PNDNFFEGKELRLKQEYFVVAATLQDIIRRFKASKFTVFDAFPDQVAIQL
NDTHPALAIPELMRIFVDIEKLPWSKAWELTQKTFAYTNHTVLPEALERW
PVDLVEKLLPRHLEIIYEINQKHLDRIVALFPKDVDRLRRMSLIEEEGSK
RINMAHLCIVGSHAVNGVAKIHSDIVKTKVFKDFSELEPDKFQNKTNGIT
PRRWLLLCNPGLAELIAEKIGEDYVKDLSQLTKLHSFLGDDVFLRELAKV
KQENKLKFSQFLETEYKVKINPSSMFDVQVKRIHEYKRQLLNCLHVITMY
NRIKKDPKKLFVPRTVIIGGKAAPGYHMAKMIIKLITSVADVVNNDPMVG
SKLKVIFLENYRVSLAEKVIPATDLSEQISTAGTEASGTGNMKFMLNGAL
TIGTMDGANVEMAEEAGEENLFIFGMRIDDVAALDKKGYEAKEYYEALPE
LKLVIDQIDNGFFSPKQPDLFKDIINMLFYHDRFKVFADYEAYVKCQDKV
SQLYMNPKAWNTMVLKNIAASGKFSSDRTIKEYAQNIWNVEPSD

3D structure

PDB

3cem Thermodynamic characterization of allosteric glycogen phosphorylase inhibitors.

Chain

Resolution

2.47 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)	H340 K531 R532 K537 T639 K643
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	AVD	B	L39 V40 K41 V45	L17 V18 K19 V23	MOAD: Kd=24nM
BS02	NBG	B	G135 L136 N284 H377 N484 E672 A673 S674 G675	G113 L114 N254 H340 N447 E635 A636 S637 G638
BS03	PLP	B	G134 G135 W491 K568 Y648 R649 V650 G675 T676 G677 K680	G112 G113 W454 K531 Y611 R612 V613 G638 T639 G640 K643
BS04	AVD	B	W67 Y75 R193 R242 R309 R310	W45 Y53 R171 R220 R279 R280	MOAD: Kd=24nM

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

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Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:3cem, PDBe:3cem, PDBj:3cem
PDBsum	3cem
PubMed	18373353
UniProt	P06737\|PYGL_HUMAN Glycogen phosphorylase, liver form (Gene Name=PYGL)

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