Structure of PDB 5ts5 Chain D Binding Site BS02

Receptor Information
>5ts5 Chain D (length=479) Species: 8725 (Bothrops atrox) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PLEECFRETDYEEFLEIAKNGLSTTSNPKRVVIVGAGMSGLSAAYVLANA
GHQVTVLEASERAGGRVKTYRNEKEGWYANLGPMRLPEKHRIVREYIRKF
DLQLNEFSQENENAWYFIKNIRKRVGEVNKDPGVLEYPVKPSEVGKSAGQ
LYEESLQKAVEELRRTNCSYMLNKYDTYSTKEYLLKEGNLSPGAVDMIGD
LLNEDSGYYVSFIESLKHDDIFAYEKRFDEIVGGMDKLPTSMYQAIQEKV
HLNARVIKIQQDVKEVTVTYQTSEKETLSVTADYVIVCTTSRAARRIKFE
PPLPPKKAHALRSVHYRSGTKIFLTCTKKFWEDDGIHGGKSTTDLPSRFI
YYPNHNFPNGVGVIIAYGIGDDANYFQALDFEDCGDIVINDLSLIHQLPK
EEIQAICRPSMIQRWSLDKYAMGGITTFTPYQFQHFSEALTAPVDRIYFA
GEYTAQAHGWIDSTIKSGLRAARDVNRAS
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 chain5ts5 Chain D Residue 501 [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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PDB5ts5 Crystal structure and molecular dynamics studies of L-amino acid oxidase from Bothrops atrox.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		G40 S44 L62 E63 A64 G70 R71 G87 P88 R90 R260 V261 T294 A298 Y372 W420 G429 I430 G456 E457 G464 W465 I466 T469
Binding residue
(residue number reindexed from 1)		G35 S39 L57 E58 A59 G65 R66 G82 P83 R85 R255 V256 T289 A293 Y367 W415 G424 I425 G451 E452 G459 W460 I461 T464
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) P92 H223 K326
Catalytic site (residue number reindexed from 1) P87 H218 K321
Enzyme Commision number 1.4.3.2: L-amino-acid oxidase.
Gene Ontology
Molecular Function
GO:0001716 L-amino-acid oxidase activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0090729 toxin activity
GO:0106329 L-phenylalaine oxidase activity
Biological Process
GO:0006915 apoptotic process
GO:0009063 amino acid catabolic process
GO:0031640 killing of cells of another organism
GO:0042742 defense response to bacterium
GO:0044478 envenomation resulting in positive regulation of platelet aggregation in another organism
GO:0044532 modulation of apoptotic process in another organism
GO:0050829 defense response to Gram-negative bacterium
GO:0050830 defense response to Gram-positive bacterium
GO:0090330 regulation of platelet aggregation
Cellular Component
GO:0005576 extracellular region

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5ts5, PDBe:5ts5, PDBj:5ts5
PDBsum5ts5
PubMed28137621
UniProtP0CC17|OXLA_BOTAT L-amino-acid oxidase

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