Structure of PDB 2vr0 Chain E Binding Site BS01

Receptor Information
>2vr0 Chain E (length=495) Species: 882 (Nitratidesulfovibrio vulgaris str. Hildenborough) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AGCSDVSTELKTPVYKTKLTAEEIRNSAFKPEFPKQYASYERNDETTVMT
EYKGSVPFNKNDNVNPLPEGYRHAQPYLKNLWLGYPFMYEYREARGHTYA
IQDFLHIDRINRYAEKGGLPATCWNCKTPKMMEWVKESGDGFWAKDVNEF
RDKIDMKDHTIGCATCHDPQTMELRITSVPLTDYLVSQGKDPKKLPRNEM
RALVCGQCHVEYYFNGPTMGVNKKPVFPWAEGFDPADMYRYYDKHGDLQV
KGFEGKFADWTHPASKTPMIKAQHPEYETWINGTHGAAGVTCADCHMSYT
RSDDKKKISSHWWTSPMKDPEMRACRQCHSDKTPDYLKSRVLFTQKRTFD
LLLAAQEVSVKAHEAVRLANEYQGAKAAGYDDLMIQAREMVRKGQFFWDY
VSAENSVGFHNPAKALDTLAQSQQFSQKAIDLAMEATQYGIGKDLSGDIK
TIVPPILKMNRKLQQDPEFMKTHKWFQYLPVLPKADQVWDGQKRL
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 chain2vr0 Chain D Residue 1005 [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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PDB2vr0 Quinol Oxidation by C-Type Cytochromes: Structural Characterization of the Menaquinol Binding Site of Nrfha.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		H353 K356
Binding residue
(residue number reindexed from 1)		H329 K332
Annotation score1
Enzymatic activity
Enzyme Commision number 1.7.2.2: nitrite reductase (cytochrome; ammonia-forming).
Gene Ontology
Molecular Function
GO:0042279 nitrite reductase (cytochrome, ammonia-forming) activity
Cellular Component
GO:0042597 periplasmic space

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:2vr0, PDBe:2vr0, PDBj:2vr0
PDBsum2vr0
PubMed18597779
UniProtQ72EF3|NRFA_NITV2 Cytochrome c nitrite reductase subunit NrfA (Gene Name=nrfA)

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