Structure of PDB 2jim Chain A Binding Site BS01

Receptor Information
>2jim Chain A (length=720) Species: 876 (Desulfovibrio desulfuricans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RPEKWVKGVCRYCGTGCGVLVGVKDGKAVAIQGNPNNHNAGLLCLKGSLL
IPVLNSKERVTQPLVRRHKGGKLEPVSWDEALDLMASRFRSSIDMYGPNS
VAWYGSGQCLTEESYVANKIFKGGFGTNNVDGNPRLCMASAVGGYVTSFG
KDEPMGTYADIDQATCFFIIGSNTSEAHPVLFRRIARRKQVEPGVKIIVA
DPRRTNTSRIADMHVAFRPGTDLAFMHSMAWVIINEELDNPRFWQRYVNF
MDAEGKPSDFEGYKAFLENYRPEKVAEICRVPVEQIYGAARAFAESAATM
SLWCMGINQRVQGVFANNLIHNLHLITGQICRPGATSFSLTGQPNACGGV
RDGGALSHLLPAGRAIPNAKHRAEMEKLWGLPEGRIAPEPGYHTVALFEA
LGRGDVKCMIICETNPAHTLPNLNKVHKAMSHPESFIVCIEAFPDAVTLE
YADLVLPPAFWCERDGVYGCGERRYSLTEKAVDPPGQCRPTVNTLVEFAR
RAGVDPQLVNFRNAEDVWNEWRMVSKGTTYDFWGMTRERLRKESGLIWPC
PSEDHPGTSLRYVRGQDPCVPADHPDRFFFYGKPDGRAVIWMRPAKGAAE
EPDAEYPLYLTSMRVIDHWHTATMTGKVPELQKANPIAFVEINEEDAART
GIKHGDSVIVETRRDAMELPARVSDVCRPGLIAVPFFDPKKLVNKLFLDA
TDPVSREPEYKICAARVRKA
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 chain2jim Chain A 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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PDB2jim Periplasmic Nitrate Reductase Revisited: A Sulfur Atom Completes the Sixth Coordination of the Catalytic Molybdenum.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		C13 C16 T18 C20 L46 C47 V183
Binding residue
(residue number reindexed from 1)		C10 C13 T15 C17 L43 C44 V180
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K49 S109 C140 M141 A180 M308 T344 G345 Q346
Catalytic site (residue number reindexed from 1) K46 S106 C137 M138 A177 M305 T341 G342 Q343
Enzyme Commision number 1.9.6.1: nitrate reductase (cytochrome).
Gene Ontology
Molecular Function
GO:0005506 iron ion 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:0042128 nitrate assimilation
Cellular Component
GO:0042597 periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2jim, PDBe:2jim, PDBj:2jim
PDBsum2jim
PubMed18327621
UniProtP81186|NAPA_DESDA Periplasmic nitrate reductase (Gene Name=napA)

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