Structure of PDB 1dy7 Chain B Binding Site BS01

Receptor Information
>1dy7 Chain B (length=536) Species: 82367 (Paracoccus pantotrophus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LAQQDVAAPGAPEGVSALSDAQYNEANKIYFERCAGCHGVLRKGATGKAL
TPDLTRDLGFDYLQSFITYGSPAGMPNWGTSGELSAEQVDLMANYLLLDP
AAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIAL
IDGATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPT
TVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKI
QSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLD
NLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIED
TGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKI
LDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGD
GSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESAL
VVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY
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 chain1dy7 Chain B Residue 601 [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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PDB1dy7 Proton-Coupled Structural Changes Upon Binding of Carbon Monoxide to Cytochrome Cd(1): A Combined Flash Photolysis and X-Ray Crystallography Study
Resolution1.6 Å
Binding residue
(original residue number in PDB)		C65 C68 H69 G78 K79 L81 Y93 F97 I98 S102 A104 G105 M106 P107 W109
Binding residue
(residue number reindexed from 1)		C34 C37 H38 G47 K48 L50 Y62 F66 I67 S71 A73 G74 M75 P76 W78
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C65 C68 H69 M106 H345 H388
Catalytic site (residue number reindexed from 1) C34 C37 H38 M75 H314 H357
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:1dy7, PDBe:1dy7, PDBj:1dy7
PDBsum1dy7
PubMed10998233
UniProtP72181|NIRS_PARPN Nitrite reductase (Gene Name=nirS)

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