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Ligand · SQD

SQD · 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol

SQD, 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol (C41 H78 O12 S, 795.1 g/mol), in the MolNFT structures on GenesisL1: bound in 72 records (67 PDB entries). Every binding site with its residues within 4.5 Å, the…

Component
SQD
Formula
C41 H78 O12 S
Class
ligand
Structures
72
PDB entries
67

Binding sites

SQD in 72 structures; the first of them:

  • 5KAF · RT XFEL structure of Photosystem II in the dark state at 3.0 A resolution · SQD A603 · binds LEU200, ALA203, GLY204, PHE265, ASN266, ASN267, SER270, PHE273 and 14 more
  • 5MX2 · Photosystem II depleted of the Mn4CaO5 cluster at 2.55 A resolution · SQD A409 · binds LEU200, ALA203, PHE265, ASN267, SER270, PHE273, PHE274, ALA277 and 10 more
  • 6HQB · Monomeric cyanobacterial photosystem I · SQD B5008 · binds LEU148, PHE151, TRP154, LEU155, GLN158, LYS160, PHE161
  • 6J3Z · Structure of C2S1M1-type PSII-FCPII supercomplex from diatom · SQD A406 · binds ALA200, PHE265, ASN267, ALA270, PHE273, PHE274, LEU277, TRP278 and 8 more
  • 6KAD · Cryo-EM structure of the C2S2M2L2-type PSII-LHCII supercomplex from Chlamydomonas… · SQD A412 · binds ASN267, SER270, PHE273, PHE274, ALA277, TRP278, ALA22, TRP24 and 5 more
  • 6KHJ · Supercomplex for electron transfer · SQD B601 · binds LEU416, VAL419, ILE420, TYR423, LYS430, GLN163, TYR164, THR167 and 16 more
  • 7D0J · Photosystem I-LHCI-LHCII of Chlamydomonas reinhardtii · SQD B850 · binds TRP155, VAL97, TYR98, LYS101
  • 7D1T · Cryo-EM Structure of PSII at 1.95 angstrom resolution · SQD A410 · binds LEU200, ALA203, GLY204, PHE265, ASN267, SER270, PHE273, PHE274 and 11 more

Residues it binds most

PHE 405, LEU 369, ARG 359, TRP 327, VAL 240, ALA 181, ILE 235, TYR 206, ASN 210, SER 189 (residue and the binding sites it lines).

Found with

  • LHG · 1,2-dipalmitoyl-phosphatidyl-glycerole
  • BCR · Beta-carotene
  • CLA · Chlorophyll A
  • DGD · Digalactosyl diacyl glycerol (dgdg)
  • LMG · 1,2-distearoyl-monogalactosyl-diglyceride
  • HEM · Protoporphyrin IX containing Fe
  • PL9 · 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2, 6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone
  • PHO · Pheophytin A
  • BCT · Bicarbonate ion
  • FE2 · Fe (II) ion
  • CL · Chloride ion
  • LMT · Dodecyl-beta-D-maltoside

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