Structure of PDB 2akj Chain A Binding Site BS02

Receptor Information
>2akj Chain A (length=535) Species: 3562 (Spinacia oleracea) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RLEPRVEERDGFWVLKEEFRSGINPAEKVKIEKDPMKLFIEDGISDLATL
SMEEVDKSKHNKDDIDVRLKWLGLFHRRKHHYGRFMMRLKLPNGVTTSEQ
TRYLASVIKKYGKDGCADVTTRQNWQIRGVVLPDVPEIIKGLESVGLTSL
QSGMDNVRNPVGNPLAGIDPHEIVDTRPFTNLISQFVTANSRGNLSITNL
PRKWNPCVIGSHDLYEHPHINDLAYMPATKNGKFGFNLLVGGFFSIKRCE
EAIPLDAWVSAEDVVPVCKAMLEAFRDLGFRGNRQKCRMMWLIDELGMEA
FRGEVEKRMPEQVLERASSEELVQKDWERREYLGVHPQKQQGLSFVGLHI
PVGRLQADEMEELARIADVYGSGELRLTVEQNIIIPNVENSKIDSLLNEP
LLKERYSPEPPILMKGLVACTGSQFCGQAIIETKARALKVTEEVQRLVSV
TRPVRMHWTGCPNSCGQVQVADIGFMGCMTRDENGKPCEGADVFVGGRIG
SDSHLGDIYKKAVPCKDLVPVVAEILINQFGAVPR
Ligand information
Ligand IDSRM
InChIInChI=1S/C42H46N4O16.Fe/c1-41(17-39(59)60)23(5-9-35(51)52)29-14-27-21(11-37(55)56)19(3-7-33(47)48)25(43-27)13-26-20(4-8-34(49)50)22(12-38(57)58)28(44-26)15-31-42(2,18-40(61)62)24(6-10-36(53)54)30(46-31)16-32(41)45-29;/h13-16,23-24H,3-12,17-18H2,1-2H3,(H10,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62);/q;+2/p-2/t23?,24-,41+,42+;/m1./s1
InChIKeyDLKSSIHHLYNIKN-MWBYXLBFSA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C[C@@]1(C(C2=[N]3C1=Cc4c(c(c5n4[Fe]36N7C(=C5)C(=C(C7=CC8=[N]6C(=C2)[C@@](C8CCC(=O)O)(C)CC(=O)O)CC(=O)O)CCC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O
ACDLabs 10.04O=C(O)CCC=6C7=Cc1c(c(c2n1[Fe]84N5C(=CC3=C(CCC(=O)O)C(C(=C2)N34)(C)CC(=O)O)C(C(=C5C=C(C=6CC(=O)O)N78)CCC(=O)O)(C)CC(=O)O)CC(=O)O)CCC(=O)O
OpenEye OEToolkits 2.0.7CC1(C(C2=[N]3C1=Cc4c(c(c5n4[Fe]36N7C(=C5)C(=C(C7=CC8=[N]6C(=C2)C(C8CCC(=O)O)(C)CC(=O)O)CC(=O)O)CCC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O
CACTVS 3.385C[C@]1(CC(O)=O)[C@@H](CCC(O)=O)C2=NC1=CC3=NC(=Cc4n5[Fe][N@@]6C(=C2)C(=C(CCC(O)=O)C6=Cc5c(CCC(O)=O)c4CC(O)=O)CC(O)=O)[C@@](C)(CC(O)=O)[C@@H]3CCC(O)=O
CACTVS 3.385C[C]1(CC(O)=O)[CH](CCC(O)=O)C2=NC1=CC3=NC(=Cc4n5[Fe][N]6C(=C2)C(=C(CCC(O)=O)C6=Cc5c(CCC(O)=O)c4CC(O)=O)CC(O)=O)[C](C)(CC(O)=O)[CH]3CCC(O)=O
FormulaC42 H44 Fe N4 O16
NameSIROHEME
ChEMBL
DrugBank
ZINC
PDB chain2akj Chain A Residue 564 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2akj Structure of Spinach Nitrite Reductase: Implications for Multi-electron Reactions by the Iron-Sulfur:Siroheme Cofactor
Resolution2.8 Å
Binding residue
(original residue number in PDB)		R98 R109 T141 T142 R143 N145 Q147 R149 R223 K224 N226 F264 F265 S266 Q306 R309 C441 T442 N484 C486 Q488
Binding residue
(residue number reindexed from 1)		R77 R88 T120 T121 R122 N124 Q126 R128 R202 K203 N205 F243 F244 S245 Q285 R288 C420 T421 N463 C465 Q467
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R109 L125 R179 R223 K224 N226 C441 C447 G481 C482 C486 G487
Catalytic site (residue number reindexed from 1) R88 L104 R158 R202 K203 N205 C420 C426 G460 C461 C465 G466
Enzyme Commision number 1.7.7.1: ferredoxin--nitrite reductase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0020037 heme binding
GO:0046872 metal ion binding
GO:0048307 ferredoxin-nitrite reductase activity
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0042128 nitrate assimilation
Cellular Component
GO:0009507 chloroplast

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2akj, PDBe:2akj, PDBj:2akj
PDBsum2akj
PubMed16331965
UniProtP05314|NIR_SPIOL Ferredoxin--nitrite reductase, chloroplastic (Gene Name=NIR)

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