Structure of PDB 6qun Chain R Binding Site BS01

Receptor Information

>6qun Chain R (length=334) Species: 3702 (Arabidopsis thaliana)

KIRIGINGFGRIGRLVARVVLQRDDVELVAVNDPFITTEYMTYMFKYDSV
HGQWKHNELKIKDEKTLLFGEKPVTVFGIRNPEDIPWAEAGADYVVESTG
VFTDKDKAAAHLKGGAKKVVISAPSKDAPMFVVGVNEHEYKSDLDIVSNA
SCTTNCLAPLAKVINDRFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGR
AASFNIIPSSTGAAKAVGKVLPALNGKLTGMSFRVPTVDVSVVDLTVRLE
KAATYDEIKKAIKEESEGKLKGILGYTEDDVVSTDFVGDNRSSIFDAKAG
IALSDKFVKLVSWYDNEWGYSSRVVDLIVHMSKA

Ligand information

• Ligand ID: NAD
• InChI: InChI=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
• InChIKey: BAWFJGJZGIEFAR-NNYOXOHSSA-N
• SMILES:
  CACTVS 3.341: NC(=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 1.5.0: c1cc(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 3.341: NC(=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 1.5.0: c1cc(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
• Formula: C21 H27 N7 O14 P2
• Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
• ChEMBL: CHEMBL1234613
• DrugBank: DB14128
• PDB chain: 6qun Chain R Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6qun Glutathionylation primes soluble glyceraldehyde-3-phosphate dehydrogenase for late collapse into insoluble aggregates.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): N6 G7 G9 R10 I11 N31 D32 P33 T96 G97 F99 S119 A149 A180 N313 Y317
• Binding residue (residue number reindexed from 1): N7 G8 G10 R11 I12 N32 D33 P34 T99 G100 F102 S122 A152 A183 N316 Y320
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): C149 H176
• Catalytic site (residue number reindexed from 1): C152 H179
• Enzyme Commision number: 1.2.1.12: glyceraldehyde-3-phosphate dehydrogenase (phosphorylating).

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
• GO:0005507 copper ion binding
• GO:0005515 protein binding
• GO:0008886 glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity
• GO:0016491 oxidoreductase activity
• 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
• GO:1901149 salicylic acid binding

Biological Process

• GO:0006006 glucose metabolic process
• GO:0006094 gluconeogenesis
• GO:0006096 glycolytic process
• GO:0006979 response to oxidative stress
• GO:0009408 response to heat
• GO:0009744 response to sucrose
• GO:0010154 fruit development
• GO:0042542 response to hydrogen peroxide
• GO:0045893 positive regulation of DNA-templated transcription
• GO:0048316 seed development
• GO:0051775 response to redox state

Cellular Component

• GO:0000325 plant-type vacuole
• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005740 mitochondrial envelope
• GO:0005794 Golgi apparatus
• GO:0005829 cytosol
• GO:0005886 plasma membrane
• GO:0009507 chloroplast
• GO:0048046 apoplast

External links

• PDB: RCSB:6qun, PDBe:6qun, PDBj:6qun
• PDBsum: 6qun
• PubMed: 31772010
• UniProt: P25858|G3PC1_ARATH Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic (Gene Name=GAPC1)