Structure of PDB 5d0f Chain B Binding Site BS13

Receptor Information
>5d0f Chain B (length=1526) Species: 284593 (Nakaseomyces glabratus CBS 138) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AHRTLLLRLSDSGEPVTSCSYGQGVLTLPSLPLPQGKKLGDMPVYTVKLA
IPAGSPVTRDGLIWTNCPPDFSTQFDREKFYKKIIKTSFHEDDHIDLDIY
VPGTYCFYLSFKNDKDELETTRKFYFVVLPILSVNDKFIPLNSIAMQSVV
SKWMGPTIKDWEKVFARVASKKYNMIHFTPLQHRGESNSPYSIYDQLEFD
PTVFKSEKEVADMVERLRTEHNILSLTDIVFNHTANNSQWLLDHPEAGYN
HKTSPHLISAIELDKKLLDFSEQMEALGYPVDLKTVDDLIKVMDGIKEHV
IGELKLWEFYVVDVKQTVSELREKWGNSKSWSDDNIPSKDDSTNLAQFVR
DNATEPGFGSLGERGSNKINIDKFAAILKKLHSEDYNNGIEELATKILND
INLPFYKEYDDDINEVLEQLFNRIKYLRIDDHGPKQGPITKKLPLSEPYF
TRFKAKDGEEYALANNGWIWDGNPLVDFASSQSKAYLRREVIVWGDCVKL
RYGKGPSDSPYLWERMSKYVEMNARIFNGFRIDNCHSTPLHVGQYFLDVA
RRVNPNLYVVAQLFSGSEAMDCLFVERLGISSLIREAMQAWSEEELSRLV
HRHGGRPIGSYKFVPLDDFPYPADVKIDEEYCAYNPDDHSVKCVSEIMIP
KTLTATPPHALFMDCTHDNETPNQKRTVEDTLPNAALVAFCSSAIGSVYG
YDEVFPQLLDLVQEKRTYSCAENTGISKVKTLLNNMREEIASEAVDIEDS
EMHVHHDGQYITFHRTNAKNGKGWYLVARTKFHSSGDQMLPRIKLSQTKA
TFKAAFSLERTGDAPISDEIIEGIPTKLRELTGFDIGFDENTKETSILLP
QDFPQGSIVIFETQQLGIDDSLDHFIRSGAIKATEKLSLESINYVLYRAE
QEEYDYSEGRSGAYDIPDYGKPVYCGLQGWVSILRKIIFYNDLAHPLSNN
LRNGHWAVDYVVNRLDLYKDKEGVAEVQEWLRSRMERIKQLPSYLVPSFF
ALVVGIMYGCCRLRAMQLMSDNVGKSTVFVQSLAMTSIQMVSAMKSTSIL
PDQNIAAMAAGLPHFSTNYMRCWGRDVFISLRGLLLTTGRYEEAKEHILA
FAKTLKHGLIPNLLDAGRNPRYNARDAAWFFVQAIQDYVTIVPGGVSLLQ
EKVTRRFPLDDEYIPYDDPKAFSYSSTIEEIIYEILNRHAGGIKYREANA
GPNLDRVMKDEGFNVEVNVDWETGLIHGGSQFNCGTWMDKMGESEKANSV
GVPGTPRDGAAVEINGLLKSCLRFVLQLSKDGKFKYTEVTKPDGSKISLS
SWNDLLQENFERCFYVPKNKEDDNKFEIDATIINRRGIYKDLYRSGKPYE
DYQFRPNFTIAMVVAPELFTPDYAAGAIELADQVLRGPVGMRTLDPSDYN
YRPYYNNGEDSDDFATSKGRNYHQGPEWVWCYGYFIRAYHYFNFLTNPKC
QVEGSAKKLKPSSYLYRKLYSRLLKHREWIENSPWAGLAELTNKDGEVCN
DSSPTQAWSTGCLLDLFYDLWISYEE
Ligand information
Ligand IDGLC
InChIInChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1
InChIKeyWQZGKKKJIJFFOK-DVKNGEFBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C1C(C(C(C(O1)O)O)O)O)O
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)O
CACTVS 3.341OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1O
ACDLabs 10.04OC1C(O)C(OC(O)C1O)CO
FormulaC6 H12 O6
Namealpha-D-glucopyranose;
alpha-D-glucose;
D-glucose;
glucose
ChEMBLCHEMBL423707
DrugBank
ZINCZINC000003861213
PDB chain5d0f Chain M Residue 5 [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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PDB5d0f Crystal structure of glycogen debranching enzyme and insights into its catalysis and disease-causing mutations.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		Q421 W472
Binding residue
(residue number reindexed from 1)		Q419 W470
Annotation score4
Enzymatic activity
Enzyme Commision number 2.4.1.25: 4-alpha-glucanotransferase.
3.2.1.33: amylo-alpha-1,6-glucosidase.
Gene Ontology
Molecular Function
GO:0004134 4-alpha-glucanotransferase activity
GO:0004135 amylo-alpha-1,6-glucosidase activity
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0016757 glycosyltransferase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0005978 glycogen biosynthetic process
GO:0005980 glycogen catabolic process
Cellular Component
GO:0005575 cellular_component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5d0f, PDBe:5d0f, PDBj:5d0f
PDBsum5d0f
PubMed27088557
UniProtQ6FSK0

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