Structure of PDB 3ubr Chain B Binding Site BS05

Receptor Information
>3ubr Chain B (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 474 [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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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)		H203 E259 W263 H268 C275 C278 H279 N298 P299 K326 G382 A385 H386
Binding residue
(residue number reindexed from 1)		H172 E228 W232 H237 C244 C247 H248 N267 P268 K295 G351 A354 H355
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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