Structure of PDB 5gpb Chain A

Receptor sequence

>5gpbA (length=833) Species: 9986 (Oryctolagus cuniculus)

RKQISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTV
RDHLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACD
EATYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGI
RYEFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHT
SQGAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNV
GGYIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIR
RFKSSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERL
DWDKAWEVTVKTCAYTNHTVIPEALERWPVHLLETLLPRHLQIIYEINQR
FLNRVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIH
SEILKKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGE
EYISDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINP
NSLFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKA
APGYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPA
ADLSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFF
IFGMRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFK
DIVNMLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSG
KFSSDRTIAQYAREIWGVEPSRQRLPAPDEKIP

3D structure

• PDB: 5gpb Comparison of the binding of glucose and glucose 1-phosphate derivatives to T-state glycogen phosphorylase b.
• Chain: A
• Resolution: 2.3 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H377 K568 R569 K574 T676 K680
• Catalytic site (residue number reindexed from 1): H368 K559 R560 K565 T667 K671
• 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	GLC	A	R426 S429 V431 E433	R417 S420 V422 E424
BS02	GLC	A	Y404 N407 V431 E433 K437	Y395 N398 V422 E424 K428
BS03	GLC	A	Y404 E405 Q408	Y395 E396 Q399
BS04	GPM	A	G135 H377 N484 K574 E672 S674 G675	G126 H368 N475 K565 E663 S665 G666
BS05	GPM	A	Q71 R193 F196 R242 R309 R310	Q62 R184 F187 R233 R300 R301
BS06	PLP	A	G134 K568 Y648 R649 V650 G675 T676 G677 K680	G125 K559 Y639 R640 V641 G666 T667 G668 K671

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0004645 1,4-alpha-oligoglucan phosphorylase activity
• GO:0008184 glycogen phosphorylase activity
• GO:0016757 glycosyltransferase activity
• GO:0030170 pyridoxal phosphate binding

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0005977 glycogen metabolic process
• GO:0005980 glycogen catabolic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0098723 skeletal muscle myofibril

External links

• PDB: RCSB:5gpb, PDBe:5gpb, PDBj:5gpb
• PDBsum: 5gpb
• PubMed: 2125493
• UniProt: P00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)