Structure of PDB 6p73 Chain A Binding Site BS01

Receptor Information
>6p73 Chain A (length=439) Species: 70863 (Shewanella oneidensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SDKTEPRNEVYKDKFKNQYNSWHDTAKSEELVDALEQDPNMVILWAGYAF
AKDYKAPRGHMYAVTDVRNTLRTGAPKNAEDGPLPMACWSCKSPDVPRLI
EEQGEDGYFKGKWAKGGPEVTNTIGCSDCHEKGSPKLRISRPYVDRALDA
IGTPFSKASKQDKESMVCAQCHVEYYFEKKEDKKGFVKFPWDMGVTVDQM
EVYYDGIEFSDWTHALSKTPMLKAQHPEYETWKMGIHGKNNVSCVDCHMP
KVTSPEGKKFTDHKVGNPFDRFEETCATCHSQTKEFLVGVTNERKAKVKE
MKLKAEEQLVKAHFEAAKAWELGATEAEMKPILTDIRHAQWRWDLAIASH
GVAAHAPEEALRVLGTSVNKAADARVKLAQLLAKKGLTDPVAIPDISTKA
KAQAVLGMDMEKMNAEKEAFKKDMLPKWDAEAKKREATY
Ligand information
Ligand IDHEC
InChIInChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,9-12H2,1-6H3,(H,39,40)(H,41,42);/q-4;+4/b21-7?,22-8?,26-13-,29-14-,30-15-,31-16-;
InChIKeyHXQIYSLZKNYNMH-LJNAALQVSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)CCC1=C(C2=CC6=C(C(=C/C)\C5=CC4=C(C(\C3=Cc7c(c(c8C=C1N2[Fe](N34)(N56)n78)CCC(=O)O)C)=C/C)C)C)C
OpenEye OEToolkits 1.5.0CC=C1C(=C2C=C3C(=CC)C(=C4N3[Fe]56N2C1=Cc7n5c(c(c7C)CCC(=O)O)C=C8N6C(=C4)C(=C8CCC(=O)O)C)C)C
CACTVS 3.341C\C=C1/C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)\C7=C/C)C=C1N2[Fe@@]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
CACTVS 3.341CC=C1C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)C7=CC)C=C1N2[Fe]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
FormulaC34 H34 Fe N4 O4
NameHEME C
ChEMBL
DrugBank
ZINC
PDB chain6p73 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6p73 Trapping of a Putative Intermediate in the CytochromecNitrite Reductase (ccNiR)-Catalyzed Reduction of Nitrite: Implications for the ccNiR Reaction Mechanism.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		K86 P88 D97 T101 R103 C119 C122 K123 C202 H203 Y206 H257
Binding residue
(residue number reindexed from 1)		K55 P57 D66 T70 R72 C88 C91 K92 C171 H172 Y175 H226
Annotation score1
Enzymatic activity
Enzyme Commision number 1.7.2.2: nitrite reductase (cytochrome; ammonia-forming).
Gene Ontology
Molecular Function
GO:0005506 iron ion binding
GO:0005509 calcium ion binding
GO:0016491 oxidoreductase activity
GO:0020037 heme binding
GO:0042279 nitrite reductase (cytochrome, ammonia-forming) activity
GO:0046872 metal ion binding
Biological Process
GO:0019645 anaerobic electron transport chain
GO:0042128 nitrate assimilation
Cellular Component
GO:0030288 outer membrane-bounded periplasmic space
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:6p73, PDBe:6p73, PDBj:6p73
PDBsum6p73
PubMed31381304
UniProtQ8EAC7|NRFA_SHEON Cytochrome c-552 (Gene Name=nrfA)

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