Structure of PDB 5lly Chain B Binding Site BS01

Receptor Information

>5lly Chain B (length=490) Species: 1036674 (Idiomarina sp. A28L)

DISKLIAACDQEPIHIPNAIQPFGAMLIVEKDTQQIVYASANSAEYFSVA
DNTIHELSDIKQANINSLLPEHLISGLASAIRENEPIWVETDRLSFLGWR
HENYYIIEVERYHVQTSNWFEIQFQRAFQKLRNCKTHNDLINTLTRLIQE
ISGYDRVMIYQFDPEWNGRVIAESVRQLFTSMLNHHFPASDIPAQARAMY
SINPIRIIPDVNAEPQPLHMIHKPQNTEAVNLSSGVLRAVSPLHMQYLRN
FGVSASTSIGIFNEDELWGIVACHHTKPRAIGRRIRRLLVRTVEFAAERL
WLIHSRNVERYMVTVQAAREQLSTTADDKHSSHEIVIEHAADWCKLFRCD
GIGYLRGEELTTYGETPDQTTINKLVEWLEENSLFWHSHMLPDGSRFLLA
IPLKSFSYLLLFRVAQNEVRTWAGKPEKLSVETSTGTMLGPRKSFEAWQD
EVSGKSQPWRTAQLYAARDIARDLLIVADSMQLNLLNDQL

Ligand information

• Ligand ID: LBV
• InChI: InChI=1S/C33H36N4O6/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/h7-8,13-15,19,35H,2,9-12H2,1,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/p+1/b20-7+,26-13-,27-14-,28-15-/t19-/m0/s1
• InChIKey: DKMLMZVDTGOEGU-ISEYCTJISA-O
• SMILES:
  OpenEye OEToolkits 1.7.2: CC=C1C(C(=O)NC1=Cc2c(c(c([nH]2)C=C3C(=C(C(=[NH+]3)C=C4C(=C(C(=O)N4)C=C)C)C)CCC(=O)O)CCC(=O)O)C)C
  OpenEye OEToolkits 1.7.2: C/C=C/1\C(C(=O)N\C1=C/c2c(c(c([nH]2)/C=C\3/C(=C(C(=[NH+]3)/C=C\4/C(=C(C(=O)N4)C=C)C)C)CCC(=O)O)CCC(=O)O)C)C
  CACTVS 3.370: CC=C1[CH](C)C(=O)NC1=Cc2[nH]c(C=C3[NH+]=C(C=C4NC(=O)C(=C4C)C=C)C(=C3CCC(O)=O)C)c(CCC(O)=O)c2C
  CACTVS 3.370: C/C=C/1[C@H](C)C(=O)NC/1=C/c2[nH]c(/C=C/3[NH+]=C(/C=C/4NC(=O)C(=C/4C)C=C)C(=C/3CCC(O)=O)C)c(CCC(O)=O)c2C
• Formula: C33 H37 N4 O6
• Name: 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid;
  2(R),3(E)- PHYTOCHROMOBILIN
• PDB chain: 5lly Chain B Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5lly Long-range allosteric signaling in red light-regulated diguanylyl cyclases.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): C17 Y168 F195 S198 D199 I200 P201 A204 R214 H252 Y255 S264 S266 H282 L464 P466
• Binding residue (residue number reindexed from 1): C9 Y160 F187 S190 D191 I192 P193 A196 R206 H244 Y247 S256 S258 H274 L439 P441
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.65: diguanylate cyclase.

Gene Ontology

Biological Process

• GO:0006355 regulation of DNA-templated transcription
• GO:0009584 detection of visible light

External links

• PDB: RCSB:5lly, PDBe:5lly, PDBj:5lly
• PDBsum: 5lly
• PubMed: 28275738
• UniProt: F7RW09