Structure of PDB 5lfa Chain A Binding Site BS01

Receptor Information
>5lfa Chain A (length=500) Species: 176299 (Agrobacterium fabrum str. C58) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SQLVLILGDQLSPSIAALDGVDKKQDTIVLCEVMAEASYVGHHKKKIAFI
FSAMRHFAEELRGEGYRVRYTRIDDADNAGSFTGEVKRAIDDLTPSRICV
TEPGEWRVRSEMDGFAGAFGIQVDIRSDRRFLSSHGEFRNWAAGRKSLTM
EYFYREMRRKTGLLMNGEQPVGGRWNFDRPKHPVFAPDKITKEVIDTVER
LFPDNFGKLENFGFAVTRTDAERALSAFIDDFLCNFGATQDAMLQDDPNL
NHSLLSFYINCGLLDALDVCKAAERAYHEGGAPLNAVEGFIRQIIGWREY
MRGIYWLAGPDYVDSNFFENDRSLPVFYWTGKTHMNCMAKVITETIENAY
AHHIQRLMITGNFALLAGIDPKAVHRWYLEVYADAYEWVELPNVIGMSQF
ADGGFLGTKPFAASGNYINRMSDYCDTCRYDPKERLGDNACPFNALYWDF
LARNREKLKSNHRLAQPYATWARMSEDVRHDLRAKAAAFLRKLDAAALEH
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 chain5lfa Chain A Residue 601 [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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PDB5lfa Crystal Structures of Bacterial (6-4) Photolyase Mutants with Impaired DNA Repair Activity.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		F249 H265 S266 L267 S269 N273 F303 Q306 I307 R311 Y363 H365 H366 R369 L370 Y391 D397 A398 V402 E403 N406
Binding residue
(residue number reindexed from 1)		F236 H252 S253 L254 S256 N260 F290 Q293 I294 R298 Y350 H352 H353 R356 L357 Y378 D384 A385 V389 E390 N393
Annotation score1
Enzymatic activity
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
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:0071949 FAD binding
Biological Process
GO:0000719 photoreactive repair
GO:0006281 DNA repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5lfa, PDBe:5lfa, PDBj:5lfa
PDBsum5lfa
PubMed27992645
UniProtA9CH39|PHRB_AGRFC (6-4) photolyase (Gene Name=phrB)

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