Structure of PDB 1qdb Chain B Binding Site BS03

Receptor Information
>1qdb Chain B (length=473) Species: 65553 (Sulfurospirillum deleyianum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GIAGKEKSEEWAKYYPRQFDSWKKTKEYDSFTDMLAKDPALVIAWSGYAF
SKDYNSPRGHYYALQDNVNSLRTGAPVDAKTGPLPTACWTCKSPDVPRLI
EEDGELEYFTGKWAKYGSQIVNVIGCANCHDDKTAELKVRVPHLNRGLQA
AGLKTFEESTHQDKRTLVCAQCHVEYYFKKTEWKDAKGADKTAMVVTLPW
ANGVGKDGNAGVEGMIKYYDEINFSDWTHNISKTPMLKAQHPGFEFWKSG
IHGQKGVSCADCHMPYTQEGSVKYSDHQVKENPLDSMDQSCMNCHRESES
KLRGIVHQKYERKEFLNKVAFDNIGKAHLETGKAIEAGASDEELKEVRKL
IRHGQFKADMAIAAHGNYFHAPEETLRLLAAGSDDAQKARLLLVKILAKH
GVMDYIAPDFDTKDKAQKLAKVDIAALAAEKMKFKQTLEQEWKKEAKAKG
RANPELYKDVDTINDGKSSWNKK
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 chain1qdb Chain B Residue 516 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1qdb Structure of cytochrome c nitrite reductase.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Y56 Q59 W63 G166 C167 C170 H171 L178 H202 R206 M305 S316 H318
Binding residue
(residue number reindexed from 1)		Y15 Q18 W22 G125 C126 C129 H130 L137 H161 R165 M264 S275 H277
Annotation score1
Enzymatic activity
Enzyme Commision number 1.7.2.2: nitrite reductase (cytochrome; ammonia-forming).
Gene Ontology
Molecular Function
GO:0005509 calcium ion binding
GO:0016491 oxidoreductase activity
GO:0020037 heme binding
GO:0042279 nitrite reductase (cytochrome, ammonia-forming) activity
GO:0046872 metal ion binding
Biological Process
GO:0019645 anaerobic electron transport chain
GO:0042128 nitrate assimilation
Cellular Component
GO:0030288 outer membrane-bounded periplasmic space
GO:0042597 periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1qdb, PDBe:1qdb, PDBj:1qdb
PDBsum1qdb
PubMed10440380
UniProtQ9Z4P4|NRFA_SULDE Cytochrome c-552 (Gene Name=nrfA)

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