Structure of PDB 3d1i Chain B Binding Site BS08

Receptor Information
>3d1i Chain B (length=519) Species: 186931 (Thioalkalivibrio nitratireducens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NLKPVDAMQCFDCHTQIEDMHTVGKHATVNCVHCHDATEHVETASSRRMG
ERPVTRMDLEACATCHTAQFNSFVEVRHESHPRLEKATPTSRSPMFDKLI
AGHGFAFEHAEPRSHAFMLVDHFVVDRAYGGRFQFKNWQKVTDGMGAVRG
AWTVLTDADPESSDQRRFLSQTATAANPVCLNCKTQDHILDWAYMGDEHE
AAKWSRTSEVVEFARDLNHPLNCFMCHDPHSAGPRVVRDGLINAVVDRGL
GTYPHDPVKSEQQGMTKVTFQRGREDFRAIGLLDTADSNVMCAQCHVEYN
CNPGYQLSDGSRVGMDDRRANHFFWANVFDYKEAAQEIDFFDFRHATTGA
ALPKLQHPEAETFWGSVHERNGVACADCHMPKVQLENGKVYTSHSQRTPR
DMMGQACLNCHAEWTEDQALYAIDYIKNYTHGKIVKSEYWLAKMIDLFPV
AKRAGVSEDVLNQARELHYDAHLYWEWWTAENSVGFHNPDQARESLMTSI
SKSKEAVSLLNDAIDAQVA
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 chain3d1i Chain B Residue 1001 [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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PDB3d1i High-resolution structural analysis of a novel octaheme cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens
Resolution1.8 Å
Binding residue
(original residue number in PDB)		C14 C17 H18 H39 A41 H44 V45 A48 S49 S50 R51 R52 M53 R56 P57 L194 Q275 R276
Binding residue
(residue number reindexed from 1)		C10 C13 H14 H35 A37 H40 V41 A44 S45 S46 R47 R48 M49 R52 P53 L190 Q271 R272
Annotation score1
Enzymatic activity
Enzyme Commision number 1.7.2.2: nitrite reductase (cytochrome; ammonia-forming).
Gene Ontology
Molecular Function
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
GO:0097164 ammonium ion metabolic process
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:3d1i, PDBe:3d1i, PDBj:3d1i
PDBsum3d1i
PubMed19393666
UniProtL0DSL2|NIR_THIND Cytochrome c-552 (Gene Name=nir)

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