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Structure of PDB 7xyl Chain D Binding Site BS02

Receptor Information
>7xyl Chain D (length=479) Species: 285500 (Streptomyces luteocolor) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VIVVGNGVLGLSVGVEIARTRPDVRVTLLGKPARQYGATPAAGAMLGAFG
EVTAHALASEHGRKKHALAVQAQRLWPEWIESLEATGTAADGRIKTADDT
VVLLNTVGHSALDDANFAAVLTALKEANAPHEEIAVESVDWIDPDPNSRP
LRALHIEGEGSVDSGILLAALERSFLQAGGRLHPVDATEIRASHGRVEGV
VTDDGDFLPAGHVVVAAGARSQRLVAALPGLAHRIPRIYDGVGVSALVDT
WDGSGPATVLRTSNRAFACGLHLVPRAGGSVYIGATNAVCLEPRGAASIE
ETVFLFNCATHQLHRGLNGSELRKVQVGSRPAPIDGFPLIGGTSVEGLWM
LSGTYRDGLHMSPLLARHVVSLMDGGTGVDGLREFRPERDLISAWSREEI
LDDVVRHTMATGYQFPWRLPLEWPHMMETFLQGPFAELADRLSDTYTPPA
DLMTAIMFSEREQQDELIAYYADVHREWH
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 chain7xyl Chain D Residue 701 [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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PDB7xyl N-Formimidoylation/-iminoacetylation modification in aminoglycosides requires FAD-dependent and ligand-protein NOS bridge dual chemistry.
Resolution2.099 Å
Binding residue
(original residue number in PDB)		V16 G17 N18 G19 V20 L21 G42 R46 Q47 G49 A50 T51 A53 A54 M57 D198 A199 A229 G230 R232 G340 R342 T366 Y367 R368 D369 G370 L371 H372
Binding residue
(residue number reindexed from 1)		V4 G5 N6 G7 V8 L9 G30 R34 Q35 G37 A38 T39 A41 A42 M45 D186 A187 A217 G218 R220 G328 R330 T354 Y355 R356 D357 G358 L359 H360
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Cellular Component
External links

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