Structure of PDB 6ndp Chain B Binding Site BS01

Receptor Information
>6ndp Chain B (length=602) Species: 314565 (Xanthomonas campestris pv. campestris str. 8004) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
CAREPIHIPGLIQPYGVLLVIDPADGRIVQASTTAADLLGVPMAALLGMP
YTQVLTLPEAQPFAVDDQPQHLMHAEVRFPQRATPPASAWVAAWHLYPQQ
WLVEMEPRDARVTLREAMPLLRSVERDPGIAEAAVRVAKGLRSLIGFDRV
MIYRFDEEWNGDIIAEARKPELEAYLGQHYPASDIPAQARALYLRNRVRQ
IADVGYQPSPIQPTVHPQLGTPVDLSDVSLRSVSPVHLEYLANMGVTATL
VASIVVNDALWGLISCHHYSPHFTNHAMRDVTDAVARTLAGRIGALQAVA
RARLESVLLTVREKLITDFNDAEHMTVELLDDMAPDLMDVVDADGVAIFH
GNDISRHGTTPDVAALRRIRDHIESEHHEALREDAVGALHVDAIGEVFPE
LADLAPLAAGFIFVPLMPQSRSALLWTRREQIQQIKWAGNPRKSFDLWQQ
TVRGRARRWSPLHLESARSLRVLIELMERKRFQQDFTLLEASLSRLRDGV
AIIERGTANAAHRLLFVNTAFADVCGSDVAELIGRELQTLYASDAPRANV
ELLQDALRNGRAAYVTLPLQVSDGAPVYRQFHLEPLPSPSGVTAHWLLQL
RD
Ligand information
Ligand IDBLA
InChIInChI=1S/C33H34N4O6/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/h7-8,13-15,34H,1-2,9-12H2,3-6H3,(H,36,43)(H,37,42)(H,38,39)(H,40,41)/b26-13-,27-14-,29-15-
InChIKeyGWZYPXHJIZCRAJ-SRVCBVSDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(c([nH]c1\C=C/2\C(=C(C(=O)N2)C=C)C)\C=C/3\C(=C(C(=N3)\C=C/4\C(=C(C(=O)N4)C)C=C)C)CCC(=O)O)CCC(=O)O
OpenEye OEToolkits 1.5.0Cc1c(c([nH]c1C=C2C(=C(C(=O)N2)C=C)C)C=C3C(=C(C(=N3)C=C4C(=C(C(=O)N4)C)C=C)C)CCC(=O)O)CCC(=O)O
CACTVS 3.341Cc1c([nH]c(C=C2N=C(C=C3NC(=O)C(=C3C=C)C)C(=C2CCC(O)=O)C)c1CCC(O)=O)C=C4NC(=O)C(=C4C)C=C
CACTVS 3.341Cc1c([nH]c(\C=C2/N=C(\C=C3/NC(=O)C(=C3C=C)C)C(=C2CCC(O)=O)C)c1CCC(O)=O)\C=C4/NC(=O)C(=C4C)C=C
FormulaC33 H34 N4 O6
NameBILIVERDINE IX ALPHA
ChEMBL
DrugBank
ZINCZINC000103534374
PDB chain6ndp Chain B Residue 900 [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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PDB6ndp Pr-favoured variants of the bacteriophytochrome from the plant pathogen Xanthomonas campestris hint on light regulation of virulence-associated mechanisms.
Resolution3.89 Å
Binding residue
(original residue number in PDB)		C13 Y168 Y195 S198 D199 I200 P201 Y208 R246 V248 S249 V251 H252 Y255 V266 H282
Binding residue
(residue number reindexed from 1)		C1 Y153 Y180 S183 D184 I185 P186 Y193 R231 V233 S234 V236 H237 Y240 V251 H267
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0009881 photoreceptor activity
Biological Process
GO:0006355 regulation of DNA-templated transcription
GO:0009584 detection of visible light

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6ndp, PDBe:6ndp, PDBj:6ndp
PDBsum6ndp
PubMed33864705
UniProtA0A0H2XCS3|BPHY_XANC8 Bacteriophytochrome (Gene Name=bphP)

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