Structure of PDB 6kgx Chain YD Binding Site BS08

Receptor Information

>6kgx Chain YD (length=237) Species: 35688 (Porphyridium purpureum)

RRTVSFNARVARNKSQAKKILEKADEFFARSVTMQYKAFACPNGVYDIQC
TEGTVKGAAYEKRAMAVSAAFRAKQASPAAKARALFENRRHAIIASHECQ
HEEDLFVRFPKLSAAYMMGKTEAMRTCSRYVVPDSLEEEYMAASVDRQMK
ERACPGGVYASSCVEGNAKGQAEQARVAALATAFRSAQKSASKTTAERYS
SAAYGRDHFAHGCSYEESVFNTYPATAAAMRSKSYNY

Ligand information

• Ligand ID: PEB
• InChI: InChI=1S/C33H40N4O6/c1-7-20-19(6)32(42)37-27(20)14-25-18(5)23(10-12-31(40)41)29(35-25)15-28-22(9-11-30(38)39)17(4)24(34-28)13-26-16(3)21(8-2)33(43)36-26/h8,14-15,19-20,26,34H,2,7,9-13H2,1,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b27-14-,29-15-/t19-,20-,26-/m1/s1
• InChIKey: NKCBCVIFPXGHAV-WAVSMFBNSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CCC1C(C(=O)NC1=CC2=NC(=Cc3c(c(c([nH]3)CC4C(=C(C(=O)N4)C=C)C)C)CCC(=O)O)C(=C2C)CCC(=O)O)C
  OpenEye OEToolkits 1.5.0: CC[C@@H]\1[C@H](C(=O)N/C1=C\C2=N/C(=C\c3c(c(c([nH]3)C[C@@H]4C(=C(C(=O)N4)C=C)C)C)CCC(=O)O)/C(=C2C)CCC(=O)O)C
  CACTVS 3.341: CC[C@@H]1[C@@H](C)C(=O)N\C1=C/C2=N\C(=C/c3[nH]c(C[C@H]4NC(=O)C(=C4C)C=C)c(C)c3CCC(O)=O)C(=C2C)CCC(O)=O
  CACTVS 3.341: CC[CH]1[CH](C)C(=O)NC1=CC2=NC(=Cc3[nH]c(C[CH]4NC(=O)C(=C4C)C=C)c(C)c3CCC(O)=O)C(=C2C)CCC(O)=O
• Formula: C33 H40 N4 O6
• Name: PHYCOERYTHROBILIN
• ZINC: ZINC000058633585
• PDB chain: 6kgx Chain YD Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6kgx Structural basis of energy transfer in Porphyridium purpureum phycobilisome.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): K90 Q102 E105 K115 M171 T174 E175 A176 C180 R182 Y183
• Binding residue (residue number reindexed from 1): K37 Q49 E52 K62 M118 T121 E122 A123 C127 R129 Y130
• Annotation score: 4

External links

• PDB: RCSB:6kgx, PDBe:6kgx, PDBj:6kgx
• PDBsum: 6kgx
• PubMed: 32076272