Structure of PDB 2j08 Chain A Binding Site BS01

Receptor Information
>2j08 Chain A (length=419) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPLLVWHRGDLRLHDHPALLEALARGPVVGLVVLDPNNLKTTPRRRAWFL
ENVRALREAYRARGGALWVLEGLPWEKVPEAARRLKAKAVYALTSHTPYG
RYRDGRVREALPVPLHLLPAPHLLPPDLPRAYRVYTPFSRLYRGAAPPLP
PPEALPKGPEEGEIPREDPGLPLPEPGEEAALAGLRAFLEAKLPRYAEER
DRLDGEGGSRLSPYFALGVLSPRLAAWEAERRGGEGARKWVAELLWRDFS
YHLLYHFPWMAERPLDPRFQAFPWQEDEALFQAWYEGKTGVPLVDAAMRE
LHATGFLSNRARMNAAQFAVKHLLLPWKRCEEAFRHLLLDGDRAVNLQGW
QWAGGLGVDAAPYFRVFNPVLQGERHDPEGRWLKRWAPEYPSYAPKDPVV
DLEEARRRYLRLARDLARG
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 chain2j08 Chain A Residue 1421 [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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PDB2j08 Natural and Non-Natural Antenna Chromophores in the DNA Photolyase from Thermus Thermophilus
Resolution2.61 Å
Binding residue
(original residue number in PDB)		Y197 S210 R211 S213 F216 W241 E244 L245 W247 R248 N310 R313 D341 G342 D343 V346 N347 Q349 G350
Binding residue
(residue number reindexed from 1)		Y196 S209 R210 S212 F215 W240 E243 L244 W246 R247 N309 R312 D340 G341 D342 V345 N346 Q348 G349
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E244 W247 W275 N310 W328 W351
Catalytic site (residue number reindexed from 1) E243 W246 W274 N309 W327 W350
Enzyme Commision number 4.1.99.3: deoxyribodipyrimidine photo-lyase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0003904 deoxyribodipyrimidine photo-lyase activity
GO:0016829 lyase activity
GO:0071949 FAD binding
GO:0097159 organic cyclic compound binding
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006281 DNA repair
GO:0006950 response to stress
GO:0009416 response to light stimulus

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2j08, PDBe:2j08, PDBj:2j08
PDBsum2j08
PubMed17051659
UniProtP61497|PHR_THET8 Deoxyribodipyrimidine photo-lyase (Gene Name=phr)

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