Structure of PDB 1h9y Chain A Binding Site BS02

Receptor Information
>1h9y Chain A (length=520) Species: 82367 (Paracoccus pantotrophus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALSDAQYNEANKIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSF
ITYGSPAGMPNWGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWK
VHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALIDGATYEIKSVLDTGY
AVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIET
SKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPE
PRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNLKTTEISAERFLHDG
GLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVH
PTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKT
HPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAG
ITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKD
ERLVTPTGKFNVYNTMTDTY
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 chain1h9y Chain A 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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PDB1h9y The Structure of an Alternative Form of Paracoccus Pantotrophus Cytochrome Cd1 Nitrite Reductase
Resolution2.4 Å
Binding residue
(original residue number in PDB)		R174 H200 I201 R216 R243 S244 I245 Y263 A301 A302 H345 R391 F444 T554 F557
Binding residue
(residue number reindexed from 1)		R127 H153 I154 R169 R196 S197 I198 Y216 A254 A255 H298 R344 F397 T507 F510
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C65 C68 H69 M106 H345 H388
Catalytic site (residue number reindexed from 1) C18 C21 H22 M59 H298 H341
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:1h9y, PDBe:1h9y, PDBj:1h9y
PDBsum1h9y
PubMed11373294
UniProtP72181|NIRS_PARPN Nitrite reductase (Gene Name=nirS)

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