Structure of PDB 2vtb Chain B Binding Site BS03

Receptor Information
>2vtb Chain B (length=491) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DHIHRVPALTEEEIDSVAIKTFERYALPSSSSVKRKGKGVTILWFRNDLR
VLDNDALYKAWSSSDTILPVYCLDPRLFHTTHFFNFPKTGALRGGFLMEC
LVDLRKNLMKRGLNLLIRSGKPEEILPSLAKDFGARTVFAHKETCSEEVD
VERLVNQGLKRVGNSTKLELIWGSTMYHKDDLPFDVFDLPDVYTQFRKSV
EAKCSIRSSTRIPLSLGPTPSVDDWGDVPTLEKLGVEPQEVTRGMRFVGG
ESAGVGRVFEYFWKKDLLKVYKETRNGMLGPDYSTKFSPWLAFGCISPRF
IYEEVQRYEKERVANNSTYWVLFELIWRDYFRFLSIKCGNSLFHLGGPRN
VNGKWSQDQKLFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQIVCSFL
VRDMGLDWRMGAEWFETCLLDYDPCSNYGNWTYGAGVNDPRYFSIPKQAQ
NYDPEGEYVAFWLQQLRRLPKEKRHWPGRLMYMDTVVPLKH
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 chain2vtb Chain B Residue 998 [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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PDB2vtb Recognition and Repair of Uv Lesions in Loop Structures of Duplex DNA by Dash-Type Cryptochrome.
Resolution2.01 Å
Binding residue
(original residue number in PDB)		Y272 S285 T286 K287 S289 L292 E325 R329 F332 F388 N391 R394 Q395 F416 D422 N428 N431 W432
Binding residue
(residue number reindexed from 1)		Y271 S284 T285 K286 S288 L291 E324 R328 F331 F387 N390 R393 Q394 F415 D421 N427 N430 W431
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E325 W328 W356 N391 W409 W432
Catalytic site (residue number reindexed from 1) E324 W327 W355 N390 W408 W431
Enzyme Commision number 4.1.99.3: deoxyribodipyrimidine photo-lyase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003904 deoxyribodipyrimidine photo-lyase activity
GO:0003913 DNA photolyase activity
GO:0005524 ATP binding
GO:0009881 photoreceptor activity
GO:0071949 FAD binding
Biological Process
GO:0000719 photoreactive repair
GO:0006139 nucleobase-containing compound metabolic process
GO:0006281 DNA repair
Cellular Component
GO:0005739 mitochondrion
GO:0009507 chloroplast

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2vtb, PDBe:2vtb, PDBj:2vtb
PDBsum2vtb
PubMed19074258
UniProtQ84KJ5|CRYD_ARATH Cryptochrome DASH, chloroplastic/mitochondrial (Gene Name=CRYD)

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