Structure of PDB 6gpb Chain A

Receptor sequence

>6gpbA (length=828) Species: 9986 (Oryctolagus cuniculus)

SVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDHL
VGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEATY
QLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEF
GIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQGA
KWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNVGGYI
QAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKS
SKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDK
AWEVTVKTCAYTNHTVIPEALERWPVHLLETLLPRHLQIIYEINQRFLNR
VAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEIL
KKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYIS
DLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLF
DVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGY
HMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLS
EQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGM
RVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVN
MLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSS
DRTIAQYAREIWGVEPSRQRLPAPDEKI

3D structure

• PDB: 6gpb Refined crystal structure of the phosphorylase-heptulose 2-phosphate-oligosaccharide-AMP complex.
• Chain: A
• Resolution: 2.86 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H377 K568 R569 K574 T676 K680
• Catalytic site (residue number reindexed from 1): H364 K555 R556 K561 T663 K667
• 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	V422 L425 R426	V409 L412 R413
BS02	GLC	A	Y404 N407 E433 K437	Y391 N394 E420 K424
BS03	GLC	A	Y404 Q408	Y391 Q395
BS04	H2P	A	G135 H377 N484 R569 Y573 K574 E672 S674 G675	G122 H364 N471 R556 Y560 K561 E659 S661 G662	PDBbind-CN: -logKd/Ki=4.85,Ki=14uM
BS05	PLP	A	K568 Y648 R649 V650 G675 T676 G677 K680	K555 Y635 R636 V637 G662 T663 G664 K667
BS06	AMP	A	F285 E572 Y613 M615	F272 E559 Y600 M602
BS07	AMP	A	Y75 R310	Y62 R297

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:6gpb, PDBe:6gpb, PDBj:6gpb
• PDBsum: 6gpb
• PubMed: 2106586
• UniProt: P00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)