Structure of PDB 4pyt Chain A Binding Site BS01

Receptor Information
>4pyt Chain A (length=302) Species: 32644 (unidentified) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDKVIQELKDLQVGKVLENEPLANHTTIKIGGPADCLVIPKDIQAVRDTM
EVVKNHGVQWRAIGRGSNLLVLDEGIRGVVIKLGAGLDHMEIDGEQVTVG
GGYSVVRLSTGISKKGLSGLEFASGIPGSVGGAVYMNAGAHGSDISRILV
KALILFEDGTMEWLTNEEMEFSYRTSILQNKRPGICLEAVLQLEQKERDA
IVAQMQKNKDYRKETQPVSNPCAGSIFRNPLPDHAGRLVEQAGLKGHRIG
GAKVSEMHGNFIVNAGGATAKDVLDLIAFIQKTIKEKYDIDMHTEVEIVG
EK
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 chain4pyt Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4pyt LucY: A Versatile New Fluorescent Reporter Protein.
Resolution1.853 Å
Binding residue
(original residue number in PDB)		R61 A62 I63 G64 R65 G66 S67 N68 I126 P127 G128 S129 G131 G132 A133 Y135 A138 G139 R174 I185 C186 R212 C222 A223 G224 E297
Binding residue
(residue number reindexed from 1)		R61 A62 I63 G64 R65 G66 S67 N68 I126 P127 G128 S129 G131 G132 A133 Y135 A138 G139 R174 I185 C186 R212 C222 A223 G224 E297
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) R174 S225 E295
Catalytic site (residue number reindexed from 1) R174 S225 E295
Enzyme Commision number 1.3.1.98: UDP-N-acetylmuramate dehydrogenase.
Gene Ontology
Molecular Function
GO:0008762 UDP-N-acetylmuramate dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0050660 flavin adenine dinucleotide binding
GO:0071949 FAD binding
Biological Process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0051301 cell division
GO:0071555 cell wall organization
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4pyt, PDBe:4pyt, PDBj:4pyt
PDBsum4pyt
PubMed25906065
UniProtQ65JX9|MURB_BACLD UDP-N-acetylenolpyruvoylglucosamine reductase (Gene Name=murB)

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