Structure of PDB 1nir Chain B Binding Site BS02

Receptor Information
>1nir Chain B (length=539) Species: 287 (Pseudomonas aeruginosa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KAAEQYQGAASAVDPAHVVRTNGAPDMSESEFNEAKQIYFQRCAGCHGVL
RKGATGKPLTPDITQQRGQQYLEALITYGTPLGMPNWGSSGELSKEQITL
MAKYIQHTPPQPPEWGMPEMRESWKVLVKPEDRPKKQLNDLDLPNLFSVT
LRDAGQIALVDGDSKKIVKVIDTGYAVHISRMSASGRYLLVIGRDARIDM
IDLWAKEPTKVAEIKIGIEARSVESSKFKGYEDRYTIAGAYWPPQFAIMD
GETLEPKQIVSTRGMTVDTQTYHPEPRVAAIIASHEHPEFIVNVKETGKV
LLVNYKDIDNLTVTSIGAAPFLHDGGWDSSHRYFMTAANNSNKVAVIDSK
DRRLSALVDVGKTPHPGRGANFVHPKYGPVWSTSHLGDGSISLIGTDPKN
HPQYAWKKVAELQGQGGGSLFIKTHPKSSHLYVDTTFNPDARISQSVAVF
DLKNLDAKYQVLPIAEWADLGEGAKRVVQPEYNKRGDEVWFSVWNGKNDS
SALVVVDDKTLKLKAVVKDPRLITPTGKFNVYNTQHDVY
Ligand information
Ligand IDDHE
InChIInChI=1S/C34H34N4O10.Fe/c1-15-17(5-7-27(39)40)21-10-22-18(6-8-28(41)42)16(2)20(36-22)11-25-33(3,13-29(43)44)32(48)24(38-25)12-26-34(4,14-30(45)46)31(47)23(37-26)9-19(15)35-21;/h9-12H,5-8,13-14H2,1-4H3,(H6,35,36,37,38,39,40,41,42,43,44,45,46,47,48);/q;+2/p-2/t33-,34-;/m1./s1
InChIKeyXLQCGNUTSJTZNF-YDXXJHAFSA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=CC6=[N]7[Fe]3(N45)[N]8=C(C=C7C(C6=O)(C)CC(=O)O)C(=O)C(C8=C2)(C)CC(=O)O)C)CCC(=O)O
OpenEye OEToolkits 2.0.7Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=CC6=[N]7[Fe]3(N45)[N]8=C(C=C7[C@@](C6=O)(C)CC(=O)O)C(=O)[C@](C8=C2)(C)CC(=O)O)C)CCC(=O)O
CACTVS 3.385CC1=C(CCC(O)=O)C2=Cc3n4[Fe][N@]2C1=CC5=NC(=CC6=NC(=Cc4c(C)c3CCC(O)=O)[C@@](C)(CC(O)=O)C6=O)[C@@](C)(CC(O)=O)C5=O
CACTVS 3.385CC1=C(CCC(O)=O)C2=Cc3n4[Fe][N]2C1=CC5=NC(=CC6=NC(=Cc4c(C)c3CCC(O)=O)[C](C)(CC(O)=O)C6=O)[C](C)(CC(O)=O)C5=O
FormulaC34 H32 Fe N4 O10
NameHEME D
ChEMBL
DrugBank
ZINC
PDB chain1nir Chain B Residue 602 [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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PDB1nir N-terminal arm exchange is observed in the 2.15 A crystal structure of oxidized nitrite reductase from Pseudomonas aeruginosa.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		R156 H182 I183 R185 R198 R225 S226 Y245 A283 A284 H327 R372 F425 F533
Binding residue
(residue number reindexed from 1)		R152 H178 I179 R181 R194 R221 S222 Y241 A279 A280 H323 R368 F421 F529
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C47 C50 H51 M88 H327 H369
Catalytic site (residue number reindexed from 1) C43 C46 H47 M84 H323 H365
Enzyme Commision number 1.7.2.1: nitrite reductase (NO-forming).
1.7.99.1: hydroxylamine reductase.
Gene Ontology
Molecular Function
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0020037 heme binding
GO:0046872 metal ion binding
GO:0050418 hydroxylamine reductase activity
GO:0050421 nitrite reductase (NO-forming) activity
Cellular Component
GO:0042597 periplasmic space

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:1nir, PDBe:1nir, PDBj:1nir
PDBsum1nir
PubMed9331415
UniProtP24474|NIRS_PSEAE Nitrite reductase (Gene Name=nirS)

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