Structure of PDB 6ebk Chain E Binding Site BS01

Receptor Information
>6ebk Chain E (length=325) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QFYRNLGKSGLRVSCLGLGTWVTFGGQITDEMAEHLMTLAYDNGINLFDT
AEVYAAGKAEVVLGNIIKKKGWRRSSLVITTKIFWGGKAETERGLSRKHI
IEGLKASLERLQLEYVDVVFANRPDPNTPMEETVRAMTHVINQGMAMYWG
TSRWSSMEIMEAYSVARQFNLIPPICEQAEYHMFQREKVEVQLPELFHKI
GVGAMTWSPLACGIVSGKYDSGIPPYSRASLKGYQWLKDKILSEEGRRQQ
AKLKELQAIAERLGCTLPQLAIAWCLRNEGVSSVLLGASNAEQLMENIGA
IQVLPKLSSSIVHEIDSILGNKPYS
Ligand information
Ligand IDNAP
InChIInChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyXJLXINKUBYWONI-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
FormulaC21 H28 N7 O17 P3
NameNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
ChEMBLCHEMBL295069
DrugBankDB03461
ZINC
PDB chain6ebk Chain E Residue 1001 [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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PDB6ebk Single-particle cryo-EM structure of a voltage-activated potassium channel in lipid nanodiscs.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		G55 W57 Y90 R189 W243 S244 P245 L246 C248 K254 R264 P304 L322 G323 S325 Q329 E332
Binding residue
(residue number reindexed from 1)		G19 W21 Y54 R153 W207 S208 P209 L210 C212 K218 R228 P268 L286 G287 S289 Q293 E296
Annotation score1
Enzymatic activity
Enzyme Commision number 1.1.1.-
Gene Ontology
Molecular Function
GO:0004033 aldo-keto reductase (NADPH) activity
GO:0005249 voltage-gated potassium channel activity
GO:0005515 protein binding
GO:0015459 potassium channel regulator activity
GO:0016491 oxidoreductase activity
GO:0044325 transmembrane transporter binding
GO:0044877 protein-containing complex binding
GO:1990002 methylglyoxal reductase (NADPH) (acetol producing) activity
Biological Process
GO:0002244 hematopoietic progenitor cell differentiation
GO:0006813 potassium ion transport
GO:0045445 myoblast differentiation
GO:0050905 neuromuscular process
GO:0055085 transmembrane transport
GO:0070995 NADPH oxidation
GO:0071805 potassium ion transmembrane transport
GO:0098900 regulation of action potential
GO:1901379 regulation of potassium ion transmembrane transport
GO:2000008 regulation of protein localization to cell surface
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005874 microtubule
GO:0005886 plasma membrane
GO:0008076 voltage-gated potassium channel complex
GO:0009898 cytoplasmic side of plasma membrane
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0030424 axon
GO:0034705 potassium channel complex
GO:0043005 neuron projection
GO:0043194 axon initial segment
GO:0043679 axon terminus
GO:0044224 juxtaparanode region of axon
GO:0045202 synapse
GO:0098839 postsynaptic density membrane
GO:0098978 glutamatergic synapse
GO:1990031 pinceau fiber

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6ebk, PDBe:6ebk, PDBj:6ebk
PDBsum6ebk
PubMed30109985
UniProtP62483|KCAB2_RAT Voltage-gated potassium channel subunit beta-2 (Gene Name=Kcnab2)

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