Structure of PDB 3ubr Chain A Binding Site BS07

Receptor Information
>3ubr 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 chain3ubr Chain B Residue 475 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ubr Laue crystal structure of Shewanella oneidensis cytochrome c nitrite reductase from a high-yield expression system.
Resolution2.59 Å
Binding residue
(original residue number in PDB)		H311 Q313
Binding residue
(residue number reindexed from 1)		H280 Q282
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:3ubr, PDBe:3ubr, PDBj:3ubr
PDBsum3ubr
PubMed22382353
UniProtQ8EAC7|NRFA_SHEON Cytochrome c-552 (Gene Name=nrfA)

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