Structure of PDB 1k08 Chain A Binding Site BS03

Receptor Information
>1k08 Chain A (length=817) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDH
LVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEAT
YQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYE
FGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQG
AKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNVGGY
IQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFK
SSKTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVK
TCAYTNHTVIPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPG
DVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKD
FYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRK
LLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRI
HEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMII
KLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAG
TEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDR
LDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDR
FKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQY
AREIWGVEPSRQRLPAP
Ligand information
Ligand IDPLP
InChIInChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
InChIKeyNGVDGCNFYWLIFO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C=O)C
FormulaC8 H10 N O6 P
NamePYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate
ChEMBLCHEMBL82202
DrugBankDB00114
ZINCZINC000001532514
PDB chain1k08 Chain A Residue 999 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1k08 Binding of N-acetyl-N '-beta-D-glucopyranosyl urea and N-benzoyl-N '-beta-D-glucopyranosyl urea to glycogen phosphorylase b: kinetic and crystallographic studies.
Resolution2.26 Å
Binding residue
(original residue number in PDB)		G134 G135 K568 Y648 R649 V650 G675 T676 K680
Binding residue
(residue number reindexed from 1)		G122 G123 K548 Y628 R629 V630 G655 T656 K660
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H357 K548 R549 K554 T656 K660
Enzyme Commision number 2.4.1.1: glycogen phosphorylase.
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1k08, PDBe:1k08, PDBj:1k08
PDBsum1k08
PubMed11895439
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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