Structure of PDB 7xmd Chain A Binding Site BS02

Receptor Information
>7xmd Chain A (length=657) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLSLDAVPFHEPIVMVTIAGIILGGLALVGLITYFGKWTYLWKEWLTSVD
HKRLGIMYIIVAIVMLLRGFADAIMMRSQQALASAGEAGFLPPHHYDQIF
TAHGVIMIFFVAMPFVIGLMNLVVPLQIGARDVAFPFLNNLSFWFTVVGV
ILVNVSLGVGEFAQTGWLAYPPLSGIEYSPGVGVDYWIWSLQLSGIGTTL
TGINFFVTILKMRAPGMTMFKMPVFTWASLCANVLIIASFPILTVTVALL
TLDRYLGTHFFTNDMGGNMMMYINLIWAWGHPEVYILILPVFGVFSEIAA
TFSRKRLFGYTSLVWATVCITVLSFIVWLHHFFTMGAGANVNAFFGITTM
IIAIPTGVKIFNWLFTMYQGRIVFHSAMLWTIGFIVTFSVGGMTGVLLAV
PGADFVLHNSLFLIAHFHNVIIGGVVFGCFAGMTYWWPKAFGFKLNETWG
KRAFWFWIIGFFVAFMPLYALGFMGMTRRLSQQIDPQFHTMLMIAASGAV
LIALGILCLVIQMYVSIRDRDQNRDLTGDPWGGRTLEWATSSPPPFYNFA
VVPHVHERDAFWEMKEKGEAYKKPDHYEEIHMPKNSGAGIVIAAFSTIFG
FAMIWHIWWLAIVGFAGMIITWIVKSFDEDVDYYVPVAEIEKLENQHFDE
ITKAGLK
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 chain7xmd Chain A Residue 702 [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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PDB7xmd Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases.
Resolution2.99 Å
Binding residue
(original residue number in PDB)		F73 A76 M79 R80 Q83 F103 H106 G107 M110 I111 G169 W170 I417 F420 H421 I424 I425 W460 R481 R482 I505
Binding residue
(residue number reindexed from 1)		F70 A73 M76 R77 Q80 F100 H103 G104 M107 I108 G166 W167 I414 F417 H418 I421 I422 W457 R478 R479 I502
Annotation score1
Enzymatic activity
Enzyme Commision number 7.1.1.3: ubiquinol oxidase (H(+)-transporting).
Gene Ontology
Molecular Function
GO:0004129 cytochrome-c oxidase activity
GO:0005507 copper ion binding
GO:0005515 protein binding
GO:0009055 electron transfer activity
GO:0009486 cytochrome bo3 ubiquinol oxidase activity
GO:0015078 proton transmembrane transporter activity
GO:0015453 oxidoreduction-driven active transmembrane transporter activity
GO:0016682 oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
GO:0020037 heme binding
GO:0046872 metal ion binding
GO:0048039 ubiquinone binding
Biological Process
GO:0009060 aerobic respiration
GO:0015990 electron transport coupled proton transport
GO:0019646 aerobic electron transport chain
GO:0022904 respiratory electron transport chain
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005886 plasma membrane
GO:0009319 cytochrome o ubiquinol oxidase complex
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7xmd, PDBe:7xmd, PDBj:7xmd
PDBsum7xmd
PubMed36481732
UniProtP0ABI8|CYOB_ECOLI Cytochrome bo(3) ubiquinol oxidase subunit 1 (Gene Name=cyoB)

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