Structure of PDB 1y56 Chain B Binding Site BS02

Receptor Information
>1y56 Chain B (length=374) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LPEKSEIVVIGGGIVGVTIAHELAKRGEEVTVIEKRFIGSGSTFRCGTGI
RQQFNDEANVRVMKRSVELWKKYSEEYGFSFKQTGYLFLLYDDEEVKTFK
RNIEIQNKFGVPTKLITPEEAKEIVPLLDISEVIAASWNPTDGKADPFEA
TTAFAVKAKEYGAKLLEYTEVKGFLIENNEIKGVKTNKGIIKTGIVVNAT
NAWANLINAMAGIKTKIPIEPYKHQAVITQPIKRGTINPMVISFKYGHAY
LTQTFHGGIIGGIGYEIGPTYDLTPTYEFLREVSYYFTKIIPALKNLLIL
RTWAGYYAKTPDSNPAIGRIEELNDYYIAAGFSGHGFMMAPAVGEMVAEL
ITKGKTKLPVEWYDPYRFERGELR
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 chain1y56 Chain B 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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PDB1y56 Crystal structure of a novel FAD-, FMN-, and ATP-containing L-proline dehydrogenase complex from Pyrococcus horikoshii
Resolution2.86 Å
Binding residue
(original residue number in PDB)		G12 G14 I15 V16 I34 E35 K36 S43 T44 R46 C47 G48 G50 E171 V172 T201 N202 W204 G306 Y307 Y308 G335 H336 G337 F338 M339
Binding residue
(residue number reindexed from 1)		G11 G13 I14 V15 I33 E34 K35 S42 T43 R45 C46 G47 G49 E170 V171 T200 N201 W203 G305 Y306 Y307 G334 H335 G336 F337 M338
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) F45 G48 T49 H225 P240 G306 M339
Catalytic site (residue number reindexed from 1) F44 G47 T48 H224 P239 G305 M338
Enzyme Commision number 1.5.99.8: Transferred entry: 1.5.5.2.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:1y56, PDBe:1y56, PDBj:1y56
PDBsum1y56
PubMed16027125
UniProtO59089

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