Structure of PDB 6l7p Chain D Binding Site BS03

Receptor Information

>6l7p Chain D (length=504) Species: 197221 (Thermosynechococcus vestitus BP-1)

STFPWLTTIILFPIVAALAIPFIPDPTGKGRPIRWYALAVGLIDFALIVY
AFTNFYDLNTPGMQLWESYDWIPEIGLRWSVGADGLSMPLILLTGFITTL
AILAAWPVTLKPRLFYFLMLAMYGGQIAVFAVQDMLVFFLAWELELIPVY
LLLAIWGGHKRQYAATKFILYTAGSSLFILVAGLAMAFYGDTVSFDMQTL
AAKDYALGFQLLVYAGFLVAYGVKLPIVPLHTWLPDAHGEATAPVHMLLA
GILLKMGGYALIRMNVDMLPAAHAKFAPVLVILGVVNIIYAALTSYAQRN
LKRKIAYSSISHIGFVLIGIASFTNLGMSGAVLQMVSHGLIGASLFFLVG
ATYDRTHTLILEEMGGVGQKMKKIFAMFTACSLASLALPGMSGFVAELMV
FIGFATSDAYSLPFRVIVVFLAAVGVILTPIYLLSMLREIFYGPENKELV
EHEALVDAEPREVFIIACLLVPIIGIGLYPKLLTQIYDATTGQVIARARE
VLPT

Ligand information

• Ligand ID: AJP
• InChI: InChI=1S/C56H92O29/c1-19-7-10-56(75-17-19)20(2)31-45(85-56)37(67)32-22-6-5-21-11-26(24(61)12-55(21,4)23(22)8-9-54(31,32)3)76-50-42(72)39(69)44(30(16-60)80-50)81-53-48(47(36(66)29(15-59)79-53)83-49-40(70)33(63)25(62)18-74-49)84-52-43(73)46(35(65)28(14-58)78-52)82-51-41(71)38(68)34(64)27(13-57)77-51/h19-53,57-73H,5-18H2,1-4H3/t19-,20+,21+,22-,23+,24-,25-,26-,27-,28-,29-,30-,31+,32-,33+,34-,35+,36-,37+,38+,39-,40-,41-,42-,43-,44+,45-,46+,47+,48-,49+,50-,51+,52+,53+,54-,55+,56-/m1/s1
• InChIKey: UVYVLBIGDKGWPX-KUAJCENISA-N
• SMILES:
  ACDLabs 12.01: CC1C2C(OC31CCC(C)CO3)C(O)C1C3CCC4CC(OC5OC(CO)C(OC6OC(CO)C(O)C(OC7OCC(O)C(O)C7O)C6OC6OC(CO)C(O)C(OC7OC(CO)C(O)C(O)C7O)C6O)C(O)C5O)C(O)CC4(C)C3CCC21C
  CACTVS 3.385: C[CH]1CC[C]2(OC1)O[CH]3[CH](O)[CH]4[CH]5CC[CH]6C[CH](O[CH]7O[CH](CO)[CH](O[CH]8O[CH](CO)[CH](O)[CH](O[CH]9OC[CH](O)[CH](O)[CH]9O)[CH]8O[CH]%10O[CH](CO)[CH](O)[CH](O[CH]%11O[CH](CO)[CH](O)[CH](O)[CH]%11O)[CH]%10O)[CH](O)[CH]7O)[CH](O)C[C]6(C)[CH]5CC[C]4(C)[CH]3[CH]2C
  CACTVS 3.385: C[C@@H]1CC[C@@]2(OC1)O[C@H]3[C@@H](O)[C@H]4[C@@H]5CC[C@H]6C[C@@H](O[C@@H]7O[C@H](CO)[C@H](O[C@@H]8O[C@H](CO)[C@@H](O)[C@H](O[C@@H]9OC[C@@H](O)[C@H](O)[C@H]9O)[C@H]8O[C@@H]%10O[C@H](CO)[C@H](O)[C@H](O[C@@H]%11O[C@H](CO)[C@@H](O)[C@H](O)[C@H]%11O)[C@H]%10O)[C@H](O)[C@H]7O)[C@H](O)C[C@]6(C)[C@H]5CC[C@]4(C)[C@H]3[C@@H]2C
  OpenEye OEToolkits 2.0.7: CC1CCC2(C(C3C(O2)C(C4C3(CCC5C4CCC6C5(CC(C(C6)OC7C(C(C(C(O7)CO)OC8C(C(C(C(O8)CO)O)OC9C(C(C(CO9)O)O)O)OC2C(C(C(C(O2)CO)O)OC2C(C(C(C(O2)CO)O)O)O)O)O)O)O)C)C)O)C)OC1
  OpenEye OEToolkits 2.0.7: C[C@@H]1CC[C@@]2([C@H]([C@H]3[C@@H](O2)[C@H]([C@@H]4[C@@]3(CC[C@H]5[C@H]4CC[C@@H]6[C@@]5(C[C@H]([C@@H](C6)O[C@H]7[C@@H]([C@H]([C@H]([C@H](O7)CO)O[C@H]8[C@@H]([C@H]([C@@H]([C@H](O8)CO)O)O[C@H]9[C@@H]([C@H]([C@@H](CO9)O)O)O)O[C@H]2[C@@H]([C@H]([C@H]([C@H](O2)CO)O)O[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)O)O)O)O)C)C)O)C)OC1
• Formula: C56 H92 O29
• Name: Digitonin
• PDB chain: 6l7p Chain D Residue 609

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6l7p Structural insights into NDH-1 mediated cyclic electron transfer.
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): F4 T9 F13 V16
• Binding residue (residue number reindexed from 1): F3 T8 F12 V15
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 7.1.1.-

Gene Ontology

Molecular Function

• GO:0003954 NADH dehydrogenase activity
• GO:0005515 protein binding
• GO:0008137 NADH dehydrogenase (ubiquinone) activity
• GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
• GO:0048038 quinone binding
• GO:0048039 ubiquinone binding

Biological Process

• GO:0009060 aerobic respiration
• GO:0015990 electron transport coupled proton transport
• GO:0042773 ATP synthesis coupled electron transport

Cellular Component

• GO:0009579 thylakoid
• GO:0016020 membrane
• GO:0031676 plasma membrane-derived thylakoid membrane
• GO:0042651 thylakoid membrane
• GO:0045271 respiratory chain complex I

External links

• PDB: RCSB:6l7p, PDBe:6l7p, PDBj:6l7p
• PDBsum: 6l7p
• PubMed: 32060291
• UniProt: Q8DKY0|NU4C1_THEVB NAD(P)H-quinone oxidoreductase chain 4 1 (Gene Name=ndhD1)