Structure of PDB 2cym Chain A Binding Site BS03

Receptor Information
>2cym Chain A (length=107) Species: 881 (Nitratidesulfovibrio vulgaris) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APKAPADGLKMEATKQPVVFNHSTHKSVKCGDCHHPVNGKEDYRKCGTAG
CHDSMDKKDKSAKGYYHVMHDKNTKFKSCVGCHVEVAGADAAKKKDLTGC
KKSKCHE
Ligand information
Ligand IDHEM
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,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
InChIKeyKABFMIBPWCXCRK-RGGAHWMASA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
CACTVS 3.385CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C
ACDLabs 12.01C=1c3c(c(c4C=C5C(=C(C=6C=C7C(=C(C8=CC=2C(=C(C=1N=2[Fe](n34)(N5=6)N78)CCC(=O)O)C)\C=C)C)\C=C)C)C)CCC(=O)O
FormulaC34 H32 Fe N4 O4
NamePROTOPORPHYRIN IX CONTAINING FE;
HEME
ChEMBL
DrugBankDB18267
ZINC
PDB chain2cym Chain A Residue 110 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2cym Effects of amino acid substitution on three-dimensional structure: an X-ray analysis of cytochrome c3 from Desulfovibrio vulgaris Hildenborough at 2 A resolution.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		A4 P5 F20 H22 H25 V28 C30 C33 H34 Y43 K45 C46
Binding residue
(residue number reindexed from 1)		A4 P5 F20 H22 H25 V28 C30 C33 H34 Y43 K45 C46
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0009055 electron transfer activity
GO:0020037 heme binding
GO:0046872 metal ion binding
Biological Process
GO:0009061 anaerobic respiration
Cellular Component
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:2cym, PDBe:2cym, PDBj:2cym
PDBsum2cym
PubMed1663945
UniProtP00131|CYC3_NITV2 Cytochrome c3 (Gene Name=DVU_3171)

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