Structure of PDB 6ymy Chain a Binding Site BS02

Receptor Information

>6ymy Chain a (length=530) Species: 559292 (Saccharomyces cerevisiae S288C)

WLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLHGNSQL
FNVLVVGHAVLMIFFLVMPALIGGFGNYLLPLMIGATDTAFPRINNIAFW
VLPMGLVCLVTSTLVESGAGTGWTVYPPLSSIQAHSGPSVDLAIFALHLT
SISSLLGAINFIVTTLNMRTNGMTMHKLPLFVWSIFITAFLLLLSLPVLS
AGITMLLLDRNFNTSFFEVSGGGDPILYEHLFWFFGHPEVYILIIPGFGI
ISHVVSTYSKKPVFGEISMVYAMASIGLLGFLVWSHHMYIVGLDADTRAY
FTSATMIIAIPTGIKIFSWLATIHGGSIRLATPMLYAIAFLFLFTMGGLT
GVALANASLDVAFHDTYYVVGHFHYVLSMGAIFSLFAGYYYWSPQILGLN
YNEKLAQIQFWLIFIGANVIFFPMHFLGINGMPRRIPDYPDAFAGWNYVA
SIGSFIATLSLFLFIYILYDQLVNGLNNKVNNKSVIYNKAPDFVESNTIF
NLNTVKSSSIEFLLTSPPAVHSFNTPAVQS

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: 6ymy Chain a Residue 602

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ymy Respiratory supercomplexes enhance electron transport by decreasing cytochrome c diffusion distance.
• Resolution: 3.41 Å
• Binding residue (original residue number in PDB): F19 G26 S33 R37 V59 H62 A63 M66 I67 W127 Y371 F377 H378 L381 S382 I386 L389 F390 F425 R438 R439 L465
• Binding residue (residue number reindexed from 1): F15 G22 S29 R33 V55 H58 A59 M62 I63 W123 Y367 F373 H374 L377 S378 I382 L385 F386 F421 R434 R435 L461
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H62 D92 W127 S157 S158 H241 E243 Y245 S256 H290 H291 T316 K319 R438
• Catalytic site (residue number reindexed from 1): H58 D88 W123 S153 S154 H237 E239 Y241 S252 H286 H287 T312 K315 R434
• Enzyme Commision number: 7.1.1.9: cytochrome-c oxidase.

Gene Ontology

Molecular Function

• GO:0004129 cytochrome-c oxidase activity
• GO:0005515 protein binding
• GO:0020037 heme binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006119 oxidative phosphorylation
• GO:0006123 mitochondrial electron transport, cytochrome c to oxygen
• GO:0009060 aerobic respiration
• GO:0015990 electron transport coupled proton transport
• GO:0045333 cellular respiration

Cellular Component

• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0016020 membrane
• GO:0031966 mitochondrial membrane
• GO:0045277 respiratory chain complex IV

External links

• PDB: RCSB:6ymy, PDBe:6ymy, PDBj:6ymy
• PDBsum: 6ymy
• PubMed: 33016568
• UniProt: P00401|COX1_YEAST Cytochrome c oxidase subunit 1 (Gene Name=COX1)