Structure of PDB 4u63 Chain A Binding Site BS02

Receptor Information
>4u63 Chain A (length=482) Species: 176299 (Agrobacterium fabrum str. C58) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSIASSLKTAPVIVWFRKDLRLSDNLALLAAVEHGGPVIPVYIREKSAGP
LGGAQEWWLHHSLAALSSSLEKAGGRLVLASGDAERILRDLISETGADTV
VWNRRYDPTGMATDKALKQKLRDDGLTVRSFSGQLLHEPSRLQTKSGGPY
RVYTPFWRALEGSDEPHAPADPPKSLTAPKVWPKSEKLSNWKLLPTKPDW
AKDFSDIWTPGETGALDKLDDFIDGALKGYEEGRDFPAKPATSLLSPHLA
AGEISPAAVWHATKGLSRHIASNDISRFRKEIVWREFCYHLLFHFPELGE
KNWNDSFDAFSWRDDEKSFKAWTRGMTGYPIVDAGMRQLWQHGTMHNRVR
MIVASFLIKHLLIDWRKGEKWFRDTLVDADPASNAANWQWVAGSGADASP
FFRIFNPILQGEKFDGDGDYVRRFVPELEKLERKYIHKPFEAPKDALKKA
GVELGKTYPLPIVDHGKARERALAAYAAVKKT
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 chain4u63 Chain A Residue 1002 [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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PDB4u63 The Class III Cyclobutane Pyrimidine Dimer Photolyase Structure Reveals a New Antenna Chromophore Binding Site and Alternative Photoreduction Pathways.
Resolution1.67 Å
Binding residue
(original residue number in PDB)		Y226 T238 S239 L240 L241 S242 E277 I278 R281 N343 R346 M347 F368 D374 A375 D376 S379 N380 N383 W384
Binding residue
(residue number reindexed from 1)		Y230 T242 S243 L244 L245 S246 E281 I282 R285 N347 R350 M351 F372 D378 A379 D380 S383 N384 N387 W388
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E277 W280 W308 N343 W361 W384
Catalytic site (residue number reindexed from 1) E281 W284 W312 N347 W365 W388
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: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:0009416 response to light stimulus

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4u63, PDBe:4u63, PDBj:4u63
PDBsum4u63
PubMed25784552
UniProtA9CJC9|PHRA_AGRFC Deoxyribodipyrimidine photo-lyase (Gene Name=phrA)

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