Structure of PDB 1y5l Chain A Binding Site BS01

Receptor Information
>1y5l Chain A (length=1244) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKFLDRFRYFKQKGETFADGHGQLLNTNRDWEDGYRQRWQHDKIVRSTHG
VNCTGSCSWKIYVKNGLVTWETQQTDYPRTRPDLPNHEPRGCPRGASYSW
YLYSANRLKYPMMRKRLMKMWREAKALHSDPVEAWASIIEDADKAKSFKQ
ARGRGGFVRSSWQEVNELIAASNVYTIKNYGPDRVAGFSPIPAMSMVSYA
SGARYLSLIGGTCLSFYDWYCDLPPASPQTWGEQTDVPESADWYNSSYII
AWGSNVPQTRTPDAHFFTEVRYKGTKTVAVTPDYAEIAKLCDLWLAPKQG
TDAAMALAMGHVMLREFHLDNPSQYFTDYVRRYTDMPMLVMLEERDGYYA
AGRMLRAADLVDALGQENNPEWKTVAFNTNGEMVAPNGSIGFRWGEKGKW
NLEQRDGKTGEETELQLSLLGSQDEIAEVGFPYFGGDGTEHFNKVELENV
LLHKLPVKRLQLADGSTALVTTVYDLTLANYGLERGLNDVNCATSYDDVK
AYTPAWAEQITGVSRSQIIRIAREFADNADKTHGRSMIIVGAGLNHWYHL
DMNYRGLINMLIFCGCVGQSGGGWAHYVGQEKLRPQTGWQPLAFALDWQR
PARHMNSTSYFYNHSSQWRYETVTAEELLSPMADKSRYTGHLIDFNVRAE
RMGWLPSAPQLGTNPLTIAGEAEKAGMNPVDYTVKSLKEGSIRFAAEQPE
NGKNHPRNLFIWRSNLLGSSGKGHEFMLKYLLGTEHGIQGKDLGQQGGVK
PEEVDWQDNGLEGKLDLVVTLDFRLSSTCLYSDIILPTATWYEKDDMNTS
DMHPFIHPLSAAVDPAWEAKSDWEIYKAIAKKFSEVCVGHLGKETDIVTL
PIQHDSAAELAQPLDVKDWKKGECDLIPGKTAPHIMVVERDYPATYERFT
SIGPLMEKIGNGGKGIAWNTQSEMDLLRKLNYTKAEGPAKGQPMLNTAID
AAEMILTLAPETNGQVAVKAWAALSEFTGRDHTHLALNKEDEKIRFRDIQ
AQPRKIISSPTWSGLEDEHVSYNAGYTNVHELIPWRTLSGRQQLYQDHQW
MRDFGESLLVYRPPIDTRSVKEVIGQKSNGNQEKALNFLTPHQKWGIHST
YSDNLLMLTLGRGGPVVWLSEADAKDLGIADNDWIEVFNSNGALTARAVV
SQRVPAGMTMMYHAQERIVNLPGSEITQQRGGIHNSVTRITPKPTHMIGG
YAHLAYGFNYYGTVGSNRDEFVVVRKMKNIDWLDGEGNDQVQES
Ligand information
Ligand IDMD1
InChIInChI=1S/C20H26N10O13P2S2/c21-19-26-14-8(16(34)28-19)25-5(1-23-14)12(46)13(47)6(31)2-40-44(36,37)43-45(38,39)41-3-7-10(32)11(33)18(42-7)30-4-24-9-15(30)27-20(22)29-17(9)35/h1,4-7,10-11,18,25,31-33,46-47H,2-3H2,(H,36,37)(H,38,39)(H3,21,26,28,34)(H3,22,27,29,35)/b13-12-/t5-,6-,7-,10-,11-,18-/m1/s1
InChIKeyIRGDLSAXQOKWLX-XHEYTWMPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.5c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OC[C@H](/C(=C(\[C@H]4C=NC5=C(N4)C(=O)NC(=N5)N)/S)/S)O)O)O)N=C(NC2=O)N
ACDLabs 10.04O=C2NC(=NC=1N=CC(NC=12)C(/S)=C(/S)C(O)COP(=O)(O)OP(=O)(O)OCC5OC(n4cnc3c4N=C(N)NC3=O)C(O)C5O)N
CACTVS 3.385NC1=NC2=C(N[CH](C=N2)C(S)=C(S)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5C(=O)NC(=Nc45)N)C(=O)N1
CACTVS 3.385NC1=NC2=C(N[C@H](C=N2)C(\S)=C(S)/[C@H](O)CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5C(=O)NC(=Nc45)N)C(=O)N1
OpenEye OEToolkits 1.7.5c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC(C(=C(C4C=NC5=C(N4)C(=O)NC(=N5)N)S)S)O)O)O)N=C(NC2=O)N
FormulaC20 H26 N10 O13 P2 S2
NamePHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
ChEMBL
DrugBank
ZINCZINC000195826882
PDB chain1y5l Chain A Residue 1800 [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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PDB1y5l Structural and Biochemical Characterization of a Quinol Binding Site of Escherichia coli Nitrate Reductase A
Resolution2.5 Å
Binding residue
(original residue number in PDB)		Y220 D222 H546 R713 S714 N715 S719 S720 K722 L771 D772 F773 R774 T788 W791 K794 D822 T1090 H1092 H1098 S1099 T1100 H1163 N1185 N1217
Binding residue
(residue number reindexed from 1)		Y220 D222 H546 R713 S714 N715 S719 S720 K722 L771 D772 F773 R774 T788 W791 K794 D822 T1090 H1092 H1098 S1099 T1100 H1163 N1185 N1217
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R94 P190 W219 Y220 P224 Q580
Catalytic site (residue number reindexed from 1) R94 P190 W219 Y220 P224 Q580
Enzyme Commision number 1.7.5.1: nitrate reductase (quinone).
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008940 nitrate reductase activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0043546 molybdopterin cofactor binding
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:0160182 nitrate reductase (quinone) activity
Biological Process
GO:0009061 anaerobic respiration
GO:0019645 anaerobic electron transport chain
GO:0042126 nitrate metabolic process
GO:0042128 nitrate assimilation
GO:0045333 cellular respiration
Cellular Component
GO:0005886 plasma membrane
GO:0009325 nitrate reductase complex
GO:0016020 membrane
GO:0044799 NarGHI complex
GO:1990204 oxidoreductase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1y5l, PDBe:1y5l, PDBj:1y5l
PDBsum1y5l
PubMed15615728
UniProtP09152|NARG_ECOLI Respiratory nitrate reductase 1 alpha chain (Gene Name=narG)

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