Structure of PDB 5kcm Chain A Binding Site BS01

Receptor Information
>5kcm Chain A (length=512) Species: 176299 (Agrobacterium fabrum str. C58) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SQLVLILGDQLSPSIAALDGVDKKQDTIVLCEVMAEASYVGHHKKKIAFW
FSAMRHFAEELRGEGYRVRYTRIDDADNAGSFTGEVKRAIDDLTPSRICV
TEPGEWRVRSEMDGFAGAFGIQVDIRSDRRFLSSHGEFRNWAAGRKSLTM
EYFYREMRRKTGLLMNGEQPVGGRWNFDAENRQPARPDLLRPKHPVFAPD
KITKEVIDTVERLFPDNFGKLENFGFAVTRTDAERALSAFIDDFLCNFGA
TQDAMLQDDPNLNHSLLSFYINCGLLDALDVCKAAERAYHEGGAPLNAVE
GFIRQIIGWREYMRGIYWLAGPDYVDSNFFENDRSLPVFYWTGKTHMNCM
AKVITETIENAYAHHIQRLMITGNFALLAGIDPKAVHRWYLEVYADAYEW
VELPNVIGMSQFADGGFLGTKPYAASGNYINRMSDYCDTCRYDPKERLGD
NACPFNALYWDFLARNREKLKSNHRLAQPYATWARMSEDVRHDLRAKAAA
FLRKLDAAALEH
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 chain5kcm 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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PDB5kcm Crystal Structures of Bacterial (6-4) Photolyase Mutants with Impaired DNA Repair Activity.
Resolution2.149 Å
Binding residue
(original residue number in PDB)		F249 H265 S266 L267 S269 Q306 I307 R311 Y363 H366 R369 Y391 D397 A398 V402 N406
Binding residue
(residue number reindexed from 1)		F248 H264 S265 L266 S268 Q305 I306 R310 Y362 H365 R368 Y390 D396 A397 V401 N405
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:5kcm, PDBe:5kcm, PDBj:5kcm
PDBsum5kcm
PubMed27992645
UniProtA9CH39|PHRB_AGRFC (6-4) photolyase (Gene Name=phrB)

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