Structure of PDB 6koe Chain A Binding Site BS02

Receptor Information

>6koe Chain A (length=607) Species: 1423 (Bacillus subtilis)

PLILGAQVSIALSTIAIIFVLTYFKKWKWLWSEWITTVDHKKLGIMYIIS
AVIMLFRGGVDGLMMRAQLALPNNSFLDSNHYNEIFTTHGTIMIIFMAMP
FLIGLINVVVPLQIGARDVAFPYLNNLSFWTFFVGAMLFNISFVIGGSPN
AGWTSYMPLASNDMSPGPGENYYLLGLQIAGIGTLMTGINFMVTILKMRT
KGMTLMRMPMFTWTTLITMVIIVFAFPVLTVALALLSFDRLFGAHFFTLE
AGGMPMLWANLFWIWGHPEVYIVILPAFGIFSEIISSFARKQLFGYKAMV
GSIIAISVLSFLVWTHHFFTMGNSASVNSFFSITTMAISIPTGVKIFNWL
FTMYKGRISFTTPMLWALAFIPNFVIGGVTGVMLAMAAADYQYHNTYFLV
SHFHYVLIAGTVFACFAGFIFWYPKMFGHKLNERIGKWFFWIFMIGFNIC
FFPQYFLGLQGMPRRIYTYGPNDGWTTLNFISTVGAFMMGVGFLILCYNI
YYSGVGRTLDWATSSAIPPHYNFAVLPEVKSQDAFLHMKEEKTELYPESK
FKKIHMPSNSGRPFFMSVAFGLAGFGLVFEWYWMGVVGLIGVLLCMVLRS
FEYDNGY

Ligand information

• Ligand ID: HEA
• InChI: InChI=1S/C49H58N4O6.Fe/c1-9-34-31(6)39-25-45-49(46(55)18-12-17-30(5)16-11-15-29(4)14-10-13-28(2)3)33(8)40(52-45)24-44-37(27-54)36(20-22-48(58)59)43(53-44)26-42-35(19-21-47(56)57)32(7)38(51-42)23-41(34)50-39;/h9,13,15,17,23-27,46,55H,1,10-12,14,16,18-22H2,2-8H3,(H4,50,51,52,53,54,56,57,58,59);/q;+2/p-2/b29-15+,30-17+,38-23-,39-25-,40-24-,41-23-,42-26-,43-26-,44-24-,45-25-;/t46-;/m0./s1
• InChIKey: ZGGYGTCPXNDTRV-PRYGPKJJSA-L
• SMILES:
  OpenEye OEToolkits 1.7.2: Cc1c2n3c(c1C=C)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C=O)CCC(=O)O)C(=C(C7=C2)[C@H](CC/C=C(\C)/CC/C=C(\C)/CCC=C(C)C)O)C)CCC(=O)O)C
  CACTVS 3.370: CC(C)=CCC/C(C)=C/CC/C(C)=C/CC[C@H](O)C1=C(C)C2=N3|[Fe]45|N6=C(C=c7n4c(=C2)c(C=O)c7CCC(O)=O)C(=C(C)C6=Cc8n5c(C=C13)c(C)c8C=C)CCC(O)=O
  CACTVS 3.370: CC(C)=CCCC(C)=CCCC(C)=CCC[CH](O)C1=C(C)C2=N3|[Fe]45|N6=C(C=c7n4c(=C2)c(C=O)c7CCC(O)=O)C(=C(C)C6=Cc8n5c(C=C13)c(C)c8C=C)CCC(O)=O
  OpenEye OEToolkits 1.7.2: Cc1c2n3c(c1C=C)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C=O)CCC(=O)O)C(=C(C7=C2)C(CCC=C(C)CCC=C(C)CCC=C(C)C)O)C)CCC(=O)O)C
  ACDLabs 12.01: O=C(O)CCC1=C(C2=Cc4c(c(c3C=C5C(=C(C=6C=C7C(C=O)=C(C8=CC1=N2[Fe](n34)(N5=6)N78)CCC(=O)O)C)C(O)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)C)C)/C=C)C
• Formula: C49 H56 Fe N4 O6
• Name: HEME-A
• PDB chain: 6koe Chain A Residue 1002

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6koe Structure of the cytochromeaa3-600 heme-copper menaquinol oxidase bound to inhibitor HQNO shows TM0 is part of the quinol binding site.
• Resolution: 3.75 Å
• Binding residue (original residue number in PDB): W166 W276 V283 I287 H329 H330 T348 S352 T355 G391 G394 L397 A398 H407 L412 H415 F416 V419
• Binding residue (residue number reindexed from 1): W153 W263 V270 I274 H316 H317 T335 S339 T342 G378 G381 L384 A385 H394 L399 H402 F403 V406
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H102 D131 W166 G196 T197 H280 E282 Y284 S295 H329 H330 T355 K358 R477
• Catalytic site (residue number reindexed from 1): H89 D118 W153 G183 T184 H267 E269 Y271 S282 H316 H317 T342 K345 R464
• Enzyme Commision number: 1.10.3.-

Gene Ontology

Molecular Function

• GO:0004129 cytochrome-c oxidase activity
• GO:0005507 copper ion binding
• GO:0016491 oxidoreductase 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

Biological Process

• GO:0006119 oxidative phosphorylation
• GO:0009060 aerobic respiration
• GO:0015990 electron transport coupled proton transport
• GO:0022904 respiratory electron transport chain
• GO:0042773 ATP synthesis coupled electron transport
• GO:1902600 proton transmembrane transport

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane

External links

• PDB: RCSB:6koe, PDBe:6koe, PDBj:6koe
• PDBsum: 6koe
• PubMed: 31888984
• UniProt: P34956|QOX1_BACSU Quinol oxidase subunit 1 (Gene Name=qoxB)