Structure of PDB 3fy4 Chain B Binding Site BS02

Receptor Information
>3fy4 Chain B (length=521) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSGSLIWFRKGLRVHDNPALEYASKGSEFMYPVFVIDPHYMESDPSASPG
SSRAGVNRIRFLLESLKDLDSSLKKLGSRLLVFKGEPGEVLVRCLQEWKV
KRLCFEYDTDPYYQALDVKVKDYASSTGVEVFSPVSHTLFNPAIIEKNGG
KPPLSYQSFLKVAGEPSCAKSELVMSYSSLPPIGDIGNLGISEVPSLEEL
GYKDDEQADWTPFRGGESEALKRLTKSISDKAWVANFEKPKGDPSAFLKP
ATTVMSPYLKFGCLSSRYFYQCLQNIYKDVKKHTSPPVSLLGQLLWREFF
YTTAFGTPNFDKMKGNRICKQIPWNEDHAMLAAWRDGKTGYPWIDAIMVQ
LLKWGWMHHLARHCVACFLTRGDLFIHWEQGRDVFERLLIDSDWAINNGN
WMWLSCSSFFYQFNRIYSPISFGKKYDPDGKYIRHFLPVLKDMPKQYIYE
PWTAPLSVQTKANCIVGKDYPKPMVLHDSASKECKRKMGEAYALNKKMDG
KVDEENLRDLRRKLQKDEHEE
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 chain3fy4 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3fy4 Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		K244 T257 T258 V259 M260 S261 L264 Q298 W301 R302 F305 W361 H364 R367 F390 L394 D396 D398 I401 N402 N405 W406
Binding residue
(residue number reindexed from 1)		K239 T252 T253 V254 M255 S256 L259 Q293 W296 R297 F300 W356 H359 R362 F385 L389 D391 D393 I396 N397 N400 W401
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Q298 W301 W329 H364 W383 W406
Catalytic site (residue number reindexed from 1) Q293 W296 W324 H359 W378 W401
Enzyme Commision number 4.1.99.13: (6-4)DNA photolyase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0003914 DNA (6-4) photolyase activity
GO:0016829 lyase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006281 DNA repair
GO:0006290 pyrimidine dimer repair
GO:0009411 response to UV

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3fy4, PDBe:3fy4, PDBj:3fy4
PDBsum3fy4
PubMed19359474
UniProtO48652|UVR3_ARATH (6-4)DNA photolyase (Gene Name=UVR3)

[Back to BioLiP]