Structure of PDB 5y6p Chain Y9 Binding Site BS08

Receptor Information

>5y6p Chain Y9 (length=245) Species: 35689 (Griffithsia pacifica)

VLRTVLRSPVPSGAATVYGYVGRGNISVILAKADEYMAKSVRKQYLAKSN
PYGTFGVQCTEGSVKFAADFSRIRALNAEFRAKLGSASKKTFDMYENRKN
AISNSHGCHHEETQFVGYKGVSSMYNVSKSEASGSCSRYASPETVVEAAM
LRFMDIQVKMAANPTGVYNISCNEGAARGQAEDVRVAALNAAFRQGQKSL
GKLLDEKYQQKKQGYSFAHGCNYEEGLINKYPALGAAFRSKSYGY

Ligand information

• Ligand ID: PUB
• InChI: InChI=1S/C33H42N4O6/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/h15,26-27,35H,7-14H2,1-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b28-15-/t26-,27+/m1/s1
• InChIKey: KDCCOOGTVSRCHX-YYVBKQGDSA-N
• SMILES:
  CACTVS 3.341: CCC1=C(C)C(=O)N[CH]1Cc2[nH]c(C=C3N=C(C[CH]4NC(=O)C(=C4C)CC)C(=C3CCC(O)=O)C)c(CCC(O)=O)c2C
  OpenEye OEToolkits 1.5.0: CCC1=C(C(=O)NC1Cc2c(c(c([nH]2)C=C3C(=C(C(=N3)CC4C(=C(C(=O)N4)CC)C)C)CCC(=O)O)CCC(=O)O)C)C
  OpenEye OEToolkits 1.5.0: CCC1=C(C(=O)N[C@H]1Cc2c(c(c([nH]2)\C=C/3\C(=C(C(=N3)C[C@@H]4C(=C(C(=O)N4)CC)C)C)CCC(=O)O)CCC(=O)O)C)C
  CACTVS 3.341: CCC1=C(C)C(=O)N[C@H]1Cc2[nH]c(\C=C3/N=C(C[C@H]4NC(=O)C(=C4C)CC)C(=C3CCC(O)=O)C)c(CCC(O)=O)c2C
• Formula: C33 H42 N4 O6
• Name: PHYCOUROBILIN
• ZINC: ZINC000040164449
• PDB chain: 5y6p Chain Y9 Residue 305

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): L86 A108 D109 R112
• Binding residue (residue number reindexed from 1): L46 A68 D69 R72
• Annotation score: 4

External links

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