Structure of PDB 1dnp Chain B Binding Site BS01

Receptor Information
>1dnp Chain B (length=469) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TTHLVWFRQDLRLHDNLALAAACRNSSARVLALYIATPRQWATHNMSPRQ
AELINAQLNGLQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLF
YNYQYEVNERARDVEVERALRNVVCEGFDDSVILPPGAVMTGNHEMYKVF
TPFKNAWLKRLREGMPECVAAPKVRSSGSIEPSPSITLNYPRQSFDTAHF
PVEEKAAIAQLRQFCQNGAGEYEQQRDFPAVEGTSRLSASLATGGLSPRQ
CLHRLLAEQPQALDGGAGSVWLNELIWREFYRHLITYHPSLCKHRPFIAW
TDRVQWQSNPAHLQAWQEGKTGYPIVDAAMRQLNSTGWMHNRLRMITASF
LVKDLLIDWREGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFN
PTTQGEKFDHEGEFIRQWLPELRDVPGKVVHEPWKWAQKAGVTLDYPQPI
VEHKEARVQTLAAYEAARK
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 chain1dnp Chain B Residue 472 [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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PDB1dnp Crystal structure of DNA photolyase from Escherichia coli.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		Y222 T234 S235 R236 L237 S238 W271 E274 R278 Y281 W338 N341 R344 D372 A377 N378 G381 W382
Binding residue
(residue number reindexed from 1)		Y222 T234 S235 R236 L237 S238 W271 E274 R278 Y281 W338 N341 R344 D372 A377 N378 G381 W382
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E274 W277 W306 N341 W359 W382
Catalytic site (residue number reindexed from 1) E274 W277 W306 N341 W359 W382
Enzyme Commision number 4.1.99.3: deoxyribodipyrimidine photo-lyase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0003904 deoxyribodipyrimidine photo-lyase activity
GO:0005515 protein binding
GO:0016829 lyase activity
GO:0071949 FAD binding
GO:0097159 organic cyclic compound binding
Biological Process
GO:0000719 photoreactive repair
GO:0006139 nucleobase-containing compound metabolic process
GO:0006281 DNA repair
GO:0006950 response to stress
GO:0007603 phototransduction, visible light
GO:0009416 response to light stimulus

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1dnp, PDBe:1dnp, PDBj:1dnp
PDBsum1dnp
PubMed7604260
UniProtP00914|PHR_ECOLI Deoxyribodipyrimidine photo-lyase (Gene Name=phrB)

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