Structure of PDB 1kqf Chain A Binding Site BS03

Receptor Information
>1kqf Chain A (length=982) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QARNYKLLRAKEIRNTCTYCSVGCGLLMYSLGDGAKNAREAIYHIEGDPD
HPVSRGALCPKGAGLLDYVNSENRLRYPEYRAPGSDKWQRISWEEAFSRI
AKLMKADRDANFIEKNEQGVTVNRWLSTGMLCASGASNETGMLTQKFARS
LGMLAVDNQARVCHGPTVASLAPTFGRGAMTNHWVDIKNANVVMVMGGNA
AEAHPVGFRWAMEAKNNNDATLIVVDPRFTRTASVADIYAPIRSGTDITF
LSGVLRYLIENNKINAEYVKHYTNASLLVRDDFAFEDGLFSGYDAEKRQY
DKSSWNYQLDENGYAKRDETLTHPRCVWNLLKEHVSRYTPDVVENICGTP
KADFLKVCEVLASTSAPDRTTTFLYALGWTQHTVGAQNIRTMAMIQLLLG
NMGMAGGGVNALRGHSNIQGLTDLGLLSTSLPGYLTLPSEKQVDLQSYLE
ANTPKATLADQVNYWSNYPKFFVSLMKSFYGDAAQKENNWGYDWLPKWDQ
TYDVIKYFNMMDEGKVTGYFCQGFNPVASFPDKNKVVSCLSKLKYMVVID
PLVTETSTFWQNHGESNDVDPASIQTEVFRLPSTCFAEEDGSIANSGRWL
QWHWKGQDAPGEARNDGEILAGIYHHLRELYQSEGGKGVEPLMKMSWNYK
QPHEPQSDEVAKENNGYALEDLYDANGVLIAKKGQLLSSFAHLRDDGTTA
SSCWIYTGSWTEQGNQMANRDNSDPSGLGNTLGWAWAWPLNRRVLYNRAS
ADINGKPWDPKRMLIQWNGSKWTGNDIPDFGNAAPGTPTGPFIMQPEGMG
RLFAINKMAEGPFPEHYEPIETPLGTNPLHPNVVSNPVVRLYEQDALRMG
KKEQFPYVGTTYRLTEHFHTWTKHALLNAIAQPEQFVEISETLAAAKGIN
NGDRVTVSSKRGFIRAVAVVTRRLKPLNVNGQQVETVGIPIHWGFEGVAR
KGYIANTLTPNVGDANSQTPEYKAFLVNIEKA
Ligand information
Ligand IDMGD
InChIInChI=1S/C20H26N10O13P2S2/c21-19-26-13-7(15(33)28-19)24-6-12(47)11(46)5(41-17(6)25-13)2-40-45(37,38)43-44(35,36)39-1-4-9(31)10(32)18(42-4)30-3-23-8-14(30)27-20(22)29-16(8)34/h3-6,9-10,17-18,24,31-32,46-47H,1-2H2,(H,35,36)(H,37,38)(H3,22,27,29,34)(H4,21,25,26,28,33)/t4-,5-,6+,9-,10-,17-,18-/m1/s1
InChIKeyVQAGYJCYOLHZDH-ILXWUORBSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC2=C(N[CH]3[CH](N2)O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6C(=O)NC(=Nc56)N)C(=C3S)S)C(=O)N1
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(=C(C5C(O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4C(=C([C@H]5[C@@H](O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N
ACDLabs 10.04O=C1C=2NC3C(S)=C(S)C(OC3NC=2N=C(N)N1)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c5N=C(N)NC4=O)C(O)C6O
CACTVS 3.341NC1=NC2=C(N[C@@H]3[C@H](N2)O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6C(=O)NC(=Nc56)N)C(=C3S)S)C(=O)N1
FormulaC20 H26 N10 O13 P2 S2
Name2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE;
MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE
ChEMBL
DrugBank
ZINCZINC000195757106
PDB chain1kqf Chain A Residue 1019 [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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PDB1kqf Molecular basis of proton motive force generation: structure of formate dehydrogenase-N.
Resolution1.6 Å
Binding residue
(original residue number in PDB)
K94 G230 G231 N232 A236 D259 P260 R261 S277 D280 A409 L410 G411 H415 G447 T893 Y895 R896 L897 T898 H900 F901 H902 K1006
Binding residue
(residue number reindexed from 1)
K61 G197 G198 N199 A203 D226 P227 R228 S244 D247 A376 L377 G378 H382 G414 T860 Y862 R863 L864 T865 H867 F868 H869 K973
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K94 C196 H197 L410 R446 G447 H448
Catalytic site (residue number reindexed from 1) K61 C163 H164 L377 R413 G414 H415
Enzyme Commision number 1.17.5.3: formate dehydrogenase-N.
Gene Ontology
Molecular Function
GO:0008863 formate dehydrogenase (NAD+) activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0043546 molybdopterin cofactor binding
GO:0047111 formate dehydrogenase (cytochrome-c-553) activity
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0045333 cellular respiration

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:1kqf, PDBe:1kqf, PDBj:1kqf
PDBsum1kqf
PubMed11884747
UniProtP24183|FDNG_ECOLI Formate dehydrogenase, nitrate-inducible, major subunit (Gene Name=fdnG)

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