Structure of PDB 1b4d Chain A Binding Site BS02

Receptor Information
>1b4d Chain A (length=804) 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
AKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNGYIQAVLDRNLA
ENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSKNFDAFPD
KVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVIP
EALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSLV
EEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQN
KTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAFI
RDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNCL
HVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDVVN
HDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNMKF
MLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQEY
YDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEYV
KCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSR
QRLP
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 chain1b4d Chain A Residue 999 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1b4d Effects of commonly used cryoprotectants on glycogen phosphorylase activity and structure.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G134 G135 K568 Y648 R649 V650 G675 T676 G677 K680
Binding residue
(residue number reindexed from 1)		G122 G123 K537 Y617 R618 V619 G644 T645 G646 K649
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H377 K568 R569 K574 T676 K680
Catalytic site (residue number reindexed from 1) H346 K537 R538 K543 T645 K649
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1b4d, PDBe:1b4d, PDBj:1b4d
PDBsum1b4d
PubMed10211820
UniProtP00489|PYGM_RABIT Glycogen phosphorylase, muscle form (Gene Name=PYGM)

[Back to BioLiP]