Structure of PDB 5yu3 Chain D Binding Site BS01

Receptor Information
>5yu3 Chain D (length=344) Species: 38300 (Streptomyces pristinaespiralis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
METWVLGRRDVAEVVAAVGRDELMRRIIDRLTGGLAEIGRGERHLSPLRG
GLERSEPVPGIWEWMPHREPGDHITLKTVGYSPANPARFGLPTILGTVAR
YDDTTGALTALMDGVLLTALRTGAASAVASRLLARPDSHTLGLIGTGAQA
VTQLHALSLVLPLQRALVWDTDPAHRESFARRAAFTGVSVEIAEPARIAA
EADVISTATSVAVGQGPVLPDTGVREHLHINAVGADLVGKTELPLGLLER
AFVTADHPEQALREGECQQLSADRLGPQLAHLCADPAAAAGRQDTLSVFD
STGFAFEDALAMEVFLEAAAERDLGIRVGIEHHPGDALDPYALQ
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain5yu3 Chain D Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5yu3 Structural Basis for Recognition of L-lysine, L-ornithine, and L-2,4-diamino Butyric Acid by Lysine Cyclodeaminase.
Resolution1.79 Å
Binding residue
(original residue number in PDB)		Y81 T93 I94 R121 T122 G147 A148 Q149 D170 T171 A208 T209 S210 V211 V233 G234 A235 S301 T302 G303
Binding residue
(residue number reindexed from 1)		Y81 T93 I94 R121 T122 G147 A148 Q149 D170 T171 A208 T209 S210 V211 V233 G234 A235 S301 T302 G303
Annotation score1
Enzymatic activity
Enzyme Commision number 4.3.1.12: ornithine cyclodeaminase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008473 ornithine cyclodeaminase activity
GO:0016829 lyase activity
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
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Cellular Component
External links
PDB RCSB:5yu3, PDBe:5yu3, PDBj:5yu3
PDBsum5yu3
PubMed29629557
UniProtD9UBW0

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