Structure of PDB 5y6p Chain d3 Binding Site BS09

Receptor Information

>5y6p Chain d3 (length=239) Species: 35689 (Griffithsia pacifica)

VLRSPVPSGAATVYGYVGRGNISVILAKADEYMAKSVRKQYLAKSNPYGT
FGVQCTEGSVKFAADFSRIRALNAEFRAKLGSASKKTFDMYENRKNAISN
SHGCHHEETQFVGYKGVSSMYNVSKSEASGSCSRYASPETVVEAAMLRFM
DIQVKMAANPTGVYNISCNEGAARGQAEDVRVAALNAAFRQGQKSLGKLL
DEKYQQKKQGYSFAHGCNYEEGLINKYPALGAAFRSKSY

Ligand information

• Ligand ID: PVN
• InChI: InChI=1S/C33H40N4O7/c1-7-20-15(2)25(36-33(20)44)12-23-16(3)21(8-10-29(39)40)26(34-23)14-27-22(9-11-30(41)42)17(4)24(35-27)13-28-31(19(6)38)18(5)32(43)37-28/h12,14,19,28,35,38H,7-11,13H2,1-6H3,(H,36,44)(H,37,43)(H,39,40)(H,41,42)/b25-12+,26-14-/t19?,28-/m1/s1
• InChIKey: SYEAKBPGLNVPDH-HVONXEAXSA-N
• SMILES:
  CACTVS 3.370: CCC1=C(C)C(=O)N[CH]1Cc2[nH]c(C=C3N=C(C=C4NC(=O)C(=C4C)CC)C(=C3CCC(O)=O)C)c(CCC(O)=O)c2C
  OpenEye OEToolkits 1.7.6: CCC1=C(C(=O)NC1Cc2c(c(c([nH]2)C=C3C(=C(C(=N3)C=C4C(=C(C(=O)N4)CC)C)C)CCC(=O)O)CCC(=O)O)C)C
  OpenEye OEToolkits 1.7.6: CCC1=C(C(=O)N[C@@H]1Cc2c(c(c([nH]2)/C=C\3/C(=C(C(=N3)/C=C/4\C(=C(C(=O)N4)CC)C)C)CCC(=O)O)CCC(=O)O)C)C
  CACTVS 3.370: CCC1=C(C)C(=O)N[C@@H]1Cc2[nH]c(\C=C\3N=C(\C=C/4NC(=O)C(=C/4C)CC)C(=C\3CCC(O)=O)C)c(CCC(O)=O)c2C
• Formula: C33 H40 N4 O6
• Name: PHYCOVIOLOBILIN;
  Phycoviolobilin, bound form
• PDB chain: 5y6p Chain d3 Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5y6p Structure of phycobilisome from the red alga Griffithsia pacifica
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): S111 R114 A115 A118 E171 C176 S177 R178 Y179
• Binding residue (residue number reindexed from 1): S67 R70 A71 A74 E127 C132 S133 R134 Y135
• Annotation score: 4

External links

• PDB: RCSB:5y6p, PDBe:5y6p, PDBj:5y6p
• PDBsum: 5y6p
• PubMed: 29045394