Structure of PDB 2nya Chain F Binding Site BS01

Receptor Information
>2nya Chain F (length=791) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EAIKWDKAPCRFCGTGCGVLVGTQQGRVVACQGDPDAPVNRGLNCIKGYF
LPKIMYGKDRLTQPLLRMKNGKYDKEGEFTPITWDQAFDVMEEKFKTALK
EKGPESIGMFGSGQWTIWEGYAASKLFKAGFRSNNIDPNARHCMASAVVG
FMRTFGMDEPMGCYDDIEQADAFVLWGANMAEMHPILWSRITNRRLSNQN
VTVAVLSTYQHRSFELADNGIIFTPQSDLVILNYIANYIIQNNAINQDFF
SKHVNLRKGATDIGYGLRPTHPLEKAAKNPGSDASEPMSFEDYKAFVAEY
TLEKTAEMTGVPKDQLEQLAQLYADPNKKVISYWTMGFNQHTRGVWANNL
VYNLHLLTGKISQPGCGPFSLTGQPSACGTAREVGTFAHRLPADMVVTNE
KHRDICEKKWNIPSGTIPAKIGLHAVAQDRALKDGKLNVYWTMCTNNMQA
GPNINEERMPGWRDPRNFIIVSDPYPTVSALAADLILPTAMWVEKEGAYG
NAERRTQFWRQQVQAPGEAKSDLWQLVQFSRRFKTEEVWPEDLLAKKPEL
RGKTLYEVLYATPEVSKFPVSELAEDQLNDESRELGFYLQKGLFEEYAWF
GRGHGHDLAPFDDYHKARGLRWPVVNGKETQWRYSEGNDPYVKAGEGYKF
YGKPDGKAVIFALPFEPAAEAPDEEYDLWLSTGRVLEHWHTGSMTRRVPE
LHRAFPEAVLFIHPLDAKARDLRRGDKVKVVSRRGEVISIVETRGRNRPP
QGLVYMPFFDAAQLVNKLTLDATDPLSKETDFKKCAVKLEK
Ligand information
Ligand IDSF4
InChIInChI=1S/4Fe.4S
InChIKeyLJBDFODJNLIPKO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7[S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
CACTVS 3.385S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
FormulaFe4 S4
NameIRON/SULFUR CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain2nya Chain F Residue 5001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2nya Spectropotentiometric and structural analysis of the periplasmic nitrate reductase from Escherichia coli
Resolution2.5 Å
Binding residue
(original residue number in PDB)		C10 F12 C13 T15 C17 C45 P185 I186
Binding residue
(residue number reindexed from 1)		C10 F12 C13 T15 C17 C45 P185 I186
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C143 T372 Q374
Catalytic site (residue number reindexed from 1) C143 T372 Q374
Enzyme Commision number 1.9.6.1: nitrate reductase (cytochrome).
Gene Ontology
Molecular Function
GO:0005506 iron ion binding
GO:0005515 protein binding
GO:0008940 nitrate reductase activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0030151 molybdenum ion binding
GO:0043546 molybdopterin cofactor binding
GO:0046872 metal ion binding
GO:0050140 nitrate reductase (cytochrome) activity
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0006777 Mo-molybdopterin cofactor biosynthetic process
GO:0009061 anaerobic respiration
GO:0042128 nitrate assimilation
GO:0045333 cellular respiration
Cellular Component
GO:0009325 nitrate reductase complex
GO:0030288 outer membrane-bounded periplasmic space
GO:0042597 periplasmic space
GO:1990204 oxidoreductase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2nya, PDBe:2nya, PDBj:2nya
PDBsum2nya
PubMed17130127
UniProtP33937|NAPA_ECOLI Periplasmic nitrate reductase (Gene Name=napA)

[Back to BioLiP]