Structure of PDB 5nm3 Chain B Binding Site BS01

Receptor Information
>5nm3 Chain B (length=485) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSL
NAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWP
GHLSLTVHRVGELLILEFEPTEAWDTGPHALRNAMFALESAPNLRALAEV
ATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIP
AQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPM
HMQFLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLEYLG
RLLSLQVQVKEAADVAAFRQSLREHHARVALAAAHSLSPHDTLSDPALDL
LGLMRAGGLILRFEGRWQTLGEVPPAPAVDALLAWLETQPGALVQTDALG
QLWPAGADLAPSAAGLLAISVGEGWSECLVWLRPELRLEVAWKDDLGPRH
SFDTYLEEKRGYAEPWHPGEIEEAQDLRDTLTGAL
Ligand information
Ligand IDLBV
InChIInChI=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
InChIKeyDKMLMZVDTGOEGU-ISEYCTJISA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2CC=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 1.7.2C/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 3.370CC=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 3.370C/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
FormulaC33 H37 N4 O6
Name3-[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
ChEMBL
DrugBank
ZINC
PDB chain5nm3 Chain B Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5nm3 On the (un)coupling of the chromophore, tongue interactions, and overall conformation in a bacterial phytochrome.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		C24 Y176 F203 D207 I208 P209 Y216 R254 S257 H260 F263 S272 H290 L463
Binding residue
(residue number reindexed from 1)		C18 Y167 F194 D198 I199 P200 Y207 R245 S248 H251 F254 S263 H281 L446
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.13.3: histidine kinase.
Gene Ontology
Biological Process
GO:0006355 regulation of DNA-templated transcription
GO:0009584 detection of visible light

View graph for
Biological Process
External links
PDB RCSB:5nm3, PDBe:5nm3, PDBj:5nm3
PDBsum5nm3
PubMed29622676
UniProtQ9RZA4|BPHY_DEIRA Bacteriophytochrome (Gene Name=bphP)

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