Structure of PDB 6v0a Chain F Binding Site BS02

Receptor Information
>6v0a Chain F (length=441) Species: 398767 (Trichlorobacter lovleyi SZ) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IPDGTIDPAVWGKNYPEEYQTWKDTALPTPEGKSKYKKGNDGGKVYDKLS
EYPFIALLFNGWGFGIEYNEPRGHVYMMKDQKEIDPSRLKGGGACLTCKT
PYAPQLAQKQGVTYFSQSYADAVNQIPEHQEMGVACIDCHNNKDMGLKIS
RGFTLVKALDKMGVDQTLTNQDKRSLVCAQCHVTYTIPKDANMKSQDVFF
PWDESKWGKISIENIIKKMRSDKSYGEWTQAVTGFKMAYIRHPEFEMYSN
QSVHWMAGVSCADCHMPYTKVGSKISDHRIMSPLKNDFKGCKQCHSESSE
WLKNQVITIQDRAASQYIRSGYALATVAKLFEMTHKQQAAGKQIDQKMYD
QAKFYYEEGFYRNLFFGAENSIGFHNPTEAMRILGDATMYAGKADGLLRQ
ALTKAGVDVPVKIDLELSKYTNNRGAKKLMFKPEQELKDPY
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 chain6v0a Chain F Residue 502 [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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PDB6v0a Cytochromecnitrite reductase from the bacteriumGeobacter lovleyirepresents a new NrfA subclass.
Resolution2.55 Å
Binding residue
(original residue number in PDB)		Y49 E52 W56 A170 C171 C174 H175 M180 L182 R210 M302 K311 I312 S313 H315
Binding residue
(residue number reindexed from 1)		Y15 E18 W22 A135 C136 C139 H140 M145 L147 R174 M266 K274 I275 S276 H278
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:6v0a, PDBe:6v0a, PDBj:6v0a
PDBsum6v0a
PubMed32518164
UniProtB3E641

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