Structure of PDB 3nyf Chain A Binding Site BS01

Receptor Information
>3nyf Chain A (length=381) Species: 287 (Pseudomonas aeruginosa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHHHHHPIEADYLVIGAGIAGASTGYWLSAHGRVVVLEREAQPGYHSTGR
SAAHYTVAYGTPQVRALTAASRAFFDNPPAGFCEHPLLSPRPEMVVDFSD
DPEELRRQYESGKALVPQMRLLDAEQACSIVPVLRRDKVFGATYDPTGAD
IDTDALHQGYLRGIRRNQGQVLCNHEALEIRRVDGAWEVRCDAGSYRAAV
LVNAAGAWCDAIAGLAGVRPLGLQPKRRSAFIFAPPPGIDCHDWPMLVSL
DESFYLKPDAGMLLGSPANADPVEAHDVQPEQLDIATGMYLIEEATTLTI
RRPEHTWAGLRSFVADGDLVAGYAANAEGFFWVAAQGGYGIQTSAAMGEA
SAALIRHQPLPAHLREHGLDEAMLSPRRLSP
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 chain3nyf Chain A Residue 1500 [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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PDB3nyf Conformational changes and substrate recognition in Pseudomonas aeruginosa D-arginine dehydrogenase.
Resolution1.3 Å
Binding residue
(original residue number in PDB)		I1009 G1010 G1012 I1013 A1014 L1031 E1032 R1033 H1040 S1041 T1042 R1044 S1045 A1046 H1048 E1170 A1171 A1199 G1200 W1202 I1206 G1303 R1305 Q1330 G1331 G1332 Y1333 G1334 I1335 Q1336
Binding residue
(residue number reindexed from 1)		I15 G16 G18 I19 A20 L37 E38 R39 H46 S47 T48 R50 S51 A52 H54 E176 A177 A205 G206 W208 I212 G309 R311 Q336 G337 G338 Y339 G340 I341 Q342
Annotation score1
Enzymatic activity
Enzyme Commision number 1.4.99.6: D-arginine dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008718 D-amino-acid dehydrogenase activity
GO:0016491 oxidoreductase activity
Biological Process
GO:0006525 arginine metabolic process
GO:0006527 arginine catabolic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3nyf, PDBe:3nyf, PDBj:3nyf
PDBsum3nyf
PubMed20809650
UniProtQ9HXE3|DAUA_PSEAE FAD-dependent catabolic D-arginine dehydrogenase DauA (Gene Name=dauA)

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