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BioLiP

Structure of PDB 1abb Chain B Binding Site BS03

Receptor Information
>1abb Chain B (length=823) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKQISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTV
RDHLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACD
EATYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGI
RYEFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHT
SQGAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNV
GGYIQAVLDRNLAENISRVLYPEGKELRLKQEYFVVAATLQDIIRRFKSS
KFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKA
WEVTVKTCAYTNHTVIPEALERWPVHLLETLLPRHLQIIYEINQRFLNRV
AAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILK
KTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISD
LDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFD
VQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYH
MAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSE
QISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMR
VEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNM
LMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSD
RTIAQYAREIWGVEPSRQRLPAP
Ligand information
Ligand IDPDP
InChIInChI=1S/C8H11NO9P2/c1-5-8(11)7(3-10)6(2-9-5)4-17-20(15,16)18-19(12,13)14/h2-3,11H,4H2,1H3,(H,15,16)(H2,12,13,14)
InChIKeyBLPOUZDLIYAHLN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)OP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCc1cnc(c(O)c1C=O)C
CACTVS 3.341Cc1ncc(CO[P](O)(=O)O[P](O)(O)=O)c(C=O)c1O
CACTVS 3.341Cc1ncc(CO[P@@](O)(=O)O[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)CO[P@](=O)(O)OP(=O)(O)O)C=O)O
FormulaC8 H11 N O9 P2
NamePYRIDOXAL-5'-DIPHOSPHATE
ChEMBL
DrugBank
ZINC
PDB chain1abb Chain B Residue 932 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1abb Control of phosphorylase b conformation by a modified cofactor: crystallographic studies on R-state glycogen phosphorylase reconstituted with pyridoxal 5'-diphosphate.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		W491 K568 R569 K574 R649 V650 A653 T676 G677 K680
Binding residue
(residue number reindexed from 1)		W477 K554 R555 K560 R635 V636 A639 T662 G663 K666
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H363 K554 R555 K560 T662 K666
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

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1abb, PDBe:1abb, PDBj:1abb
PDBsum1abb
PubMed1304390
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

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