Structure of PDB 1dy7 Chain A Binding Site BS01

Receptor Information
>1dy7 Chain A (length=434) Species: 82367 (Paracoccus pantotrophus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PPEFGMKEMRESWKVHVAPEDRPTQQENDWDLENLFSVTLRDAGQIALID
GATYEIKSVLDTGYAVHISRLSASGRYLFVIGRDGKVNMIDLWMKEPTTV
AEIKIGSEARSIETSKMEGWEDKYAIAGAYWPPQYVIMDGETLEPKKIQS
TRGMTYDEQEYHPEPRVAAILASHYRPEFIVNVKETGKILLVDYTDLDNL
KTTEISAERFLHDGGLDGSHRYFITAANARNKLVVIDTKEGKLVAIEDTG
GQTPHPGRGANFVHPTFGPVWATSHMGDDSVALIGTDPEGHPDNAWKILD
SFPALGGGSLFIKTHPNSQYLYVDATLNPEAEISGSVAVFDIKAMTGDGS
DPEFKTLPIAEWAGITEGQPRVVQGEFNKDGTEVWFSVWNGKDQESALVV
VDDKTLELKHVIKDERLVTPTGKFNVYNTMTDTY
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 chain1dy7 Chain A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		R174 H200 I201 R216 R243 S244 Y263 A301 A302 H345 R391 F444 W522 F557
Binding residue
(residue number reindexed from 1)		R41 H67 I68 R83 R110 S111 Y130 A168 A169 H212 R258 F311 W389 F424
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H345 H388
Catalytic site (residue number reindexed from 1) H212 H255
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
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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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