Structure of PDB 1knr Chain A Binding Site BS01

Receptor Information
>1knr Chain A (length=529) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PEHSCDVLIIGSGAAGLSLALRLADQHQVIVLSKGPVTEGSTFYAQGGIA
AVFDETDSIDSHVEDTLIAGAGICDRHAVEFVASNARSCVQWLIDQGVLF
DTHIQPNGEESYHLTREGGHSHRRILHAADATGREVETTLVSKALNHPNI
RVLERTNAVDLIVSDKIGLPGTRRVVGAWVWNRNKETVETCHAKAVVLAT
GGASKVYQYTTNPDISSGDGIAMAWRAGCRVANLEFNQFHPTALYHPQAR
NFLLTEALRGEGAYLKRPDGTRFMPDFDERGELAPRDIVARAIDHEMKRL
GADCMFLDISHKPADFIRQHFPMIYEKLLGLGIDLTQEPVPIVPAAHYTC
GGVMVDDHGRTDVEGLYAIGEVSYTGLHGANLMASNSLLECLVYGWSAAE
DITRRMPYAHDISTLPPWDESRVENPDERVVIQHNWHELRLFMWDYVGIV
RTTKRLERALRRITMLQQEIDEYYAHFRVSNNLLELRNLVQVAELIVRCA
MMRKESRGLHFTLDYPELLTHSGPSILSP
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 chain1knr Chain A Residue 800 [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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PDB1knr Structure of FAD-bound L-aspartate oxidase: insight into substrate specificity and catalysis.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		G15 A19 K38 S45 T46 Y48 A49 G51 G52 A162 A203 T204 G205 D223 L257 H351 Y352 E375 S389 S391 L392
Binding residue
(residue number reindexed from 1)		G11 A15 K34 S41 T42 Y44 A45 G47 G48 A158 A199 T200 G201 D219 L253 H347 Y348 E371 S385 S387 L388
Annotation score1
Binding affinityMOAD: Kd=8.1uM
Enzymatic activity
Catalytic site (original residue number in PDB) E121 Q242 H244 L257 E260 R263 R290 H351 Y352 L386
Catalytic site (residue number reindexed from 1) E117 Q238 H240 L253 E256 R259 R286 H347 Y348 L382
Enzyme Commision number 1.4.3.16: L-aspartate oxidase.
1.5.99.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008734 L-aspartate oxidase activity
GO:0016491 oxidoreductase activity
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0009435 NAD biosynthetic process
GO:0019363 pyridine nucleotide biosynthetic process
GO:0034628 'de novo' NAD biosynthetic process from aspartate
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1knr, PDBe:1knr, PDBj:1knr
PDBsum1knr
PubMed11863440
UniProtP10902|NADB_ECOLI L-aspartate oxidase (Gene Name=nadB)

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