Structure of PDB 1qks Chain A Binding Site BS02

Receptor Information
>1qks Chain A (length=559) Species: 82367 (Paracoccus pantotrophus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DPAAALEDHKTRTDNRYEPSLDNLAQQDVAAPGAPEGVTALSDAQYNEAN
KIYFERCAGCHGVLRKGATGKALTPDLTRDLGFDYLQSFITYASPAGMPN
WGTSGELSAEQVDLMANYLLLDPAAPPEFGMKEMRESWKVHVAPEDRPTQ
QMNDWDLENLFSVTLRDAGQIALIDGSTYEIKTVLDTGYAVHISRLSASG
RYLFVIGRDGKVNMIDLWMKEPTTVAEIKIGSEARSIETSKMEGWEDKYA
IAGAYWPPQYVIMDGETLEPKKIQSTRGMTYDEQEYHPEPRVAAILASHY
RPEFIVNVKETGKILLVDYTDLNNLKTTEISAERFLHDGGLDGSHRYFIT
AANARNKLVVIDTKEGKLVAIEDTGGQTPHPGRGANFVHPTFGPVWATSH
MGDDSVALIGTDPEGHPDNAWKILDSFPALGGGSLFIKTHPNSQYLYVDA
TLNPEAEISGSVAVFDIKAMTGDGSDPEFKTLPIAEWAGITEGQPRVVQG
EFNKDGTEVWFSVWNGKDQESALVVVDDKTLELKHVIKDERLVTPTGKFN
VYNTMTDTY
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 chain1qks 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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PDB1qks The anatomy of a bifunctional enzyme: structural basis for reduction of oxygen to water and synthesis of nitric oxide by cytochrome cd1.
Resolution1.28 Å
Binding residue
(original residue number in PDB)		Y25 E26 S28 M106 W109 R174 H200 I201 R216 R243 S244 Y263 H345 R391 F444 W522 T554 F557
Binding residue
(residue number reindexed from 1)		Y17 E18 S20 M98 W101 R166 H192 I193 R208 R235 S236 Y255 H337 R383 F436 W514 T546 F549
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C65 C68 H69 M106 H345 H388
Catalytic site (residue number reindexed from 1) C57 C60 H61 M98 H337 H380
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:1qks, PDBe:1qks, PDBj:1qks
PDBsum1qks
PubMed7736589
UniProtP72181|NIRS_PARPN Nitrite reductase (Gene Name=nirS)

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