Structure of PDB 7xmd Chain A Binding Site BS01

Receptor Information

>7xmd Chain A (length=657) Species: 562 (Escherichia coli)

KLSLDAVPFHEPIVMVTIAGIILGGLALVGLITYFGKWTYLWKEWLTSVD
HKRLGIMYIIVAIVMLLRGFADAIMMRSQQALASAGEAGFLPPHHYDQIF
TAHGVIMIFFVAMPFVIGLMNLVVPLQIGARDVAFPFLNNLSFWFTVVGV
ILVNVSLGVGEFAQTGWLAYPPLSGIEYSPGVGVDYWIWSLQLSGIGTTL
TGINFFVTILKMRAPGMTMFKMPVFTWASLCANVLIIASFPILTVTVALL
TLDRYLGTHFFTNDMGGNMMMYINLIWAWGHPEVYILILPVFGVFSEIAA
TFSRKRLFGYTSLVWATVCITVLSFIVWLHHFFTMGAGANVNAFFGITTM
IIAIPTGVKIFNWLFTMYQGRIVFHSAMLWTIGFIVTFSVGGMTGVLLAV
PGADFVLHNSLFLIAHFHNVIIGGVVFGCFAGMTYWWPKAFGFKLNETWG
KRAFWFWIIGFFVAFMPLYALGFMGMTRRLSQQIDPQFHTMLMIAASGAV
LIALGILCLVIQMYVSIRDRDQNRDLTGDPWGGRTLEWATSSPPPFYNFA
VVPHVHERDAFWEMKEKGEAYKKPDHYEEIHMPKNSGAGIVIAAFSTIFG
FAMIWHIWWLAIVGFAGMIITWIVKSFDEDVDYYVPVAEIEKLENQHFDE
ITKAGLK

Ligand information

• Ligand ID: HEO
• InChI: InChI=1S/C49H60N4O5.Fe/c1-10-35-31(6)40-26-45-49(46(54)19-13-18-30(5)17-12-16-29(4)15-11-14-28(2)3)34(9)41(53-45)24-38-32(7)36(20-22-47(55)56)43(51-38)27-44-37(21-23-48(57)58)33(8)39(52-44)25-42(35)50-40;/h10,14,16,18,24-27,46,54H,1,11-13,15,17,19-23H2,2-9H3,(H4,50,51,52,53,55,56,57,58);/q;+4/p-2/b29-16+,30-18-,38-24-,39-25-,40-26-,41-24-,42-25-,43-27-,44-27-,45-26-;/t46-;/m0./s1
• InChIKey: FRKORVCRVCLRBA-BZKSIRDQSA-L
• SMILES:
  OpenEye OEToolkits 2.0.7: Cc1c2cc3[n+]4c(cc5c(c(c6n5[Fe]47n2c(c1CCC(=O)O)cc8[n+]7c(c6)C(=C8CCC(=O)O)C)C=C)C)C(=C3C)C(CCC=C(C)CCC=C(C)CCC=C(C)C)O
  CACTVS 3.385: CC(C)=CCCC(C)=CCCC(C)=CCC[CH](O)C1=C(C)C2=[N+]3C1=Cc4n5c(C=C6C(=C(CCC(O)=O)C7=[N+]6[Fe]35[N]8C(=C2)C(=C(CCC(O)=O)C8=C7)C)C)c(C=C)c4C
  ACDLabs 12.01: [Fe]321N4C5=CC8=[N+]1C(=Cc7n2c(C=C6[N+]3=C(C=C4C(=C5CCC(=O)O)C)C(=C6C(O)CC\C=C(/CC\C=C(\CC\C=C(\C)C)C)C)C)c(c7\C=C)C)C(=C8CCC(=O)O)C
  CACTVS 3.385: CC(C)=CCC/C(C)=C/CC/C(C)=C/CC[C@H](O)C1=C(C)C2=[N@@+]3C1=Cc4n5c(C=C6C(=C(CCC(O)=O)C7=[N@@+]6[Fe@]35[N@]8C(=C2)C(=C(CCC(O)=O)C8=C7)C)C)c(C=C)c4C
  OpenEye OEToolkits 2.0.7: Cc1c2cc3[n+]4c(cc5c(c(c6n5[Fe]47n2c(c1CCC(=O)O)cc8[n+]7c(c6)C(=C8CCC(=O)O)C)C=C)C)C(=C3C)[C@H](CC/C=C(/C)\CCC=C(C)CCC=C(C)C)O
• Formula: C49 H58 Fe N4 O5
• Name: HEME O
• PDB chain: 7xmd Chain A Residue 701

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7xmd Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases.
• Resolution: 2.99 Å
• Binding residue (original residue number in PDB): W170 W280 V287 I291 H333 H334 A356 T359 G360 G395 G398 V399 L401 A402 D407 H411 L416 H419 F420 V423 I424 R481
• Binding residue (residue number reindexed from 1): W167 W277 V284 I288 H330 H331 A353 T356 G357 G392 G395 V396 L398 A399 D404 H408 L413 H416 F417 V420 I421 R478
• Annotation score: 1

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

External links

• PDB: RCSB:7xmd, PDBe:7xmd, PDBj:7xmd
• PDBsum: 7xmd
• PubMed: 36481732
• UniProt: P0ABI8|CYOB_ECOLI Cytochrome bo(3) ubiquinol oxidase subunit 1 (Gene Name=cyoB)