Structure of PDB 6k8k Chain B Binding Site BS01

Receptor Information
>6k8k Chain B (length=481) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKKTIVWFRRDLRIEDNPALAAAAHEGSVFPVFIWCPEEEGQFYPGRASR
WWMKQSLAHLSQSLKALGSDLTLIQTHNTISAILDCIRVTGPTKVVFNHL
YDPVSLVRDHTVKEKLVERGISVQSYNGDLLYEPWEIYCKPFTSFNSYWK
KCLDMSIESVMLPPPWRLMPITAAAEAIWACSIEELGLENEAEKPSNALL
TRAWSPGWSNADKLLNEFIEKQLIDYAKNSKKVVGNSTSLLSPYLHFGEI
SVRHVFQCARMKQIIWARDKNSEGEESADLFLRGIGLREYSRYICFNFPL
SHLRFFPWDADVDKFKAWRQGRTGYPLVDAGMRELWATGWMHNRIRVIVS
SFGVKFLLLPWKWGMKYFWDTLLDADLECDILGWQYISGSIPDGHELDRL
DNPALQGAKYDPEGEYIRQWLPELARLPTEWIHHPWDAPLTVLKASGVEL
GTNYAKPIVDIDTARELLAKAISRTREAQIM
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain6k8k Chain B Residue 701 [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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PDB6k8k Structural insights into BIC-mediated inactivation of Arabidopsis cryptochrome 2.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		Y232 T244 S245 L246 S248 L251 G290 I291 L293 R294 W353 N356 R359 D387 D389 C392 D393 G396
Binding residue
(residue number reindexed from 1)		Y226 T238 S239 L240 S242 L245 G284 I285 L287 R288 W340 N343 R346 D374 D376 C379 D380 G383
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) G290 L293 W321 N356 W374 W397
Catalytic site (residue number reindexed from 1) G284 L287 W308 N343 W361 W384
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0009881 photoreceptor activity
GO:0009882 blue light photoreceptor activity
GO:0016301 kinase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0071949 FAD binding
GO:0097159 organic cyclic compound binding
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006950 response to stress
GO:0006952 defense response
GO:0007623 circadian rhythm
GO:0009414 response to water deprivation
GO:0009416 response to light stimulus
GO:0009637 response to blue light
GO:0009638 phototropism
GO:0009646 response to absence of light
GO:0009785 blue light signaling pathway
GO:0009909 regulation of flower development
GO:0009911 positive regulation of flower development
GO:0010075 regulation of meristem growth
GO:0010118 stomatal movement
GO:0010244 response to low fluence blue light stimulus by blue low-fluence system
GO:0010617 circadian regulation of calcium ion oscillation
GO:0042752 regulation of circadian rhythm
GO:0046777 protein autophosphorylation
GO:0048574 long-day photoperiodism, flowering
GO:0051607 defense response to virus
GO:0072387 flavin adenine dinucleotide metabolic process
GO:1901371 regulation of leaf morphogenesis
GO:1902347 response to strigolactone
GO:2000028 regulation of photoperiodism, flowering
GO:2000379 positive regulation of reactive oxygen species metabolic process
Cellular Component
GO:0000325 plant-type vacuole
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0016604 nuclear body
GO:0016605 PML body

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6k8k, PDBe:6k8k, PDBj:6k8k
PDBsum6k8k
PubMed32398826
UniProtQ96524|CRY2_ARATH Cryptochrome-2 (Gene Name=CRY2)

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