Structure of PDB 5b13 Chain J Binding Site BS01

Receptor Information

>5b13 Chain J (length=177) Species: 2822 (Palmaria palmata)

MLDAFSRVVVNSDAKAAYVGGSDLQALKKFITDGNKRLDSVSFVVSNASC
IVSDAVSGMICENPGLIAPGGNCYTNRRMAACLRDGEIILRYASYALLAG
DPSVLEDRCLNGLKETYIALGVPTNSSVRAVSIMKASATAFVSGTASDRK
MACPDGDCSALASELGSYCDRVAAAIS

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: 5b13 Chain J Residue 203

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5b13 Structural properties of phycoerythrin from dulse palmaria palmata
• Resolution: 2.094 Å
• Binding residue (original residue number in PDB): C50 D54 G58 C61 R129 I133 A136 S137 F141 A146 S147 D148
• Binding residue (residue number reindexed from 1): C50 D54 G58 C61 R129 I133 A136 S137 F141 A146 S147 D148
• Annotation score: 4

Gene Ontology

Biological Process

• GO:0015979 photosynthesis

Cellular Component

• GO:0009507 chloroplast
• GO:0009535 chloroplast thylakoid membrane
• GO:0009579 thylakoid
• GO:0016020 membrane
• GO:0030089 phycobilisome

External links

• PDB: RCSB:5b13, PDBe:5b13, PDBj:5b13
• PDBsum: 5b13
• UniProt: F2ZAL7