Structure of PDB 3k2b Chain E Binding Site BS01

Receptor Information
>3k2b Chain E (length=336) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKLKVAINGFGRIGRNFLRCWHGRKDSPLDIIAINDTGGVKQASHLLKYD
STLGIFDADVKPSGETAISVDGKIIQVVSNRNPSLLPWKELGIDIVIEGT
GVFVDREGAGKHIEAGAKKVIITAPGKGDIPTYVVGVNADAYSHDEPIIS
NASCTTNCLAPFVKVLDQKFGIIKGTMTTTHSYTGDQRLLDASHRDLRRA
RAAALNIVPTSTGAAKAVALVLPNLKGKLNGIALRVPTPNVSVVDLVVQV
SKKTFAEEVNAAFRDSAEKELKGILDVCDEPLVSVDFRCSDFSTTIDSSL
TMVMGDDMVKVIAWYDNEWGYSQRVVDLADIVANNW
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
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)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)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)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]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)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain3k2b Chain E Residue 335 [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]
PDB3k2b Structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase (isoform A4) from Arabidopsis thaliana in complex with NAD
Resolution2.6 Å
Binding residue
(original residue number in PDB)		G7 F8 G9 R10 I11 T33 T96 G97 T119 C149 T179 Y317
Binding residue
(residue number reindexed from 1)		G9 F10 G11 R12 I13 T37 T100 G101 T123 C154 T184 Y321
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) C149 H176
Catalytic site (residue number reindexed from 1) C154 H181
Enzyme Commision number 1.2.1.13: glyceraldehyde-3-phosphate dehydrogenase (NADP(+)) (phosphorylating).
Gene Ontology
Molecular Function
GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
GO:0050661 NADP binding
GO:0051287 NAD binding
Biological Process
GO:0006006 glucose metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3k2b, PDBe:3k2b, PDBj:3k2b
PDBsum3k2b
PubMed20516587
UniProtP25856|G3PA1_ARATH Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic (Gene Name=GAPA1)

[Back to BioLiP]