Structure of PDB 1e2r Chain B Binding Site BS02

Receptor Information
>1e2r Chain B (length=543) Species: 266 (Paracoccus denitrificans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YEPSLDNLAQQDVAAPGAPEGVTALSDAQYNEANKIYFERCAGCHGVLRK
GATGKALTPDLTRDLGFDYLQSFITYASPAGMPNWGTSGELSAEQVDLMA
NYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLR
DAGQIALIDGSTYEIKTVLDTGYAVHISRLSASGRYLFVIGRDGKVNMID
LWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGE
TLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILL
VDYTDLNNLKTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEG
KLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGH
PDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFD
IKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNG
KDQESALVVVDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY
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 chain1e2r 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1e2r X-Ray Crystallographic Study of Cyanide Binding Provides Insights Into the Structure-Function Relationship for Cytochrome Cd1 Nitrite Reductase from Paracoccus Pantotrophus.
Resolution1.59 Å
Binding residue
(original residue number in PDB)		Y25 E26 P27 R174 H200 I201 R216 R243 S244 Y263 A301 A302 H345 R391 F444 W522 T554 F557
Binding residue
(residue number reindexed from 1)		Y1 E2 P3 R150 H176 I177 R192 R219 S220 Y239 A277 A278 H321 R367 F420 W498 T530 F533
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C65 C68 H69 M106 H345 H388
Catalytic site (residue number reindexed from 1) C41 C44 H45 M82 H321 H364
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:1e2r, PDBe:1e2r, PDBj:1e2r
PDBsum1e2r
PubMed10827177
UniProtP72181|NIRS_PARPN Nitrite reductase (Gene Name=nirS)

[Back to BioLiP]