Structure of PDB 2yev Chain D Binding Site BS03

Receptor Information

>2yev Chain D (length=780) Species: 300852 (Thermus thermophilus HB8)

WAVLWDLLTTVDHKKIGLMYTATAFFAFALAGVFSLLIRTQLAVPNNQFL
TGEQYNQILTLHGATMLFFFIIQAGLTGFGNFVVPLMLGARDVALPRVNA
FSYWAFLGAIVLALMSYFFPGGAPSVGWTFYYPFSAQSESGVDFYLAAIL
LLGFSSLLGNANFVATIYNLRAQGMSLWKMPIYVWSVFAASVLNLFSLAG
LTAATLLVLLERKIGLSWFNPAVGGDPVLFQQFFWFYSHPTVYVMLLPYL
GILAEVASTFARKPLFGYRQMVWAQMGIVVLGTMVWAHHMFTVGESTLFQ
IAFAFFTALIAVPTGVKLFNIIGTLWGGKLQMKTPLYWVLGFIFNFLLGG
ITGVMLSMTPLDYQFHDSYFVVAHFHNVLMAGSGFGAFAGLYYWWPKMTG
RMYDERLGRLHFWLFLVGYLLTFLPQYALGYLGMPRRYYTYNADIAGWPE
LNLLSTIGAYILGLGGLVWIYTMWKSLRSGPKAPDNPWGGYTLEWLTASP
PKAHNFDVKLPTEFPSERPLYDWKKKGVELKPEDPAHIHLPNSSFWPFYS
AATLFAFFVAVAALPVPNVWMWVFLALFAYGLVRWALEDEYSHPVEHHTV
TGKSNAWMGMAWFIVSEVGLFAILIAGYLYLRLSGAATPPEERPALWLAL
LNTFLLVSSSFTVHFAHHDLRRGRFNPFRFGLLVTIILGVLFFLVQSWEF
YQFYHHSSWQENLWTAAFFTIVGLHGLHVVIGGFGLILAYLQALRGKITL
HNHGTLEAASMYWHLVDAVWLVIVTIFYVW

Ligand information

• Ligand ID: HAS
• InChI: InChI=1S/C54H66N4O6.Fe/c1-10-39-36(7)44-29-50-54(51(60)22-14-21-35(6)20-13-19-34(5)18-12-17-33(4)16-11-15-32(2)3)38(9)45(57-50)28-49-42(31-59)41(24-26-53(63)64)48(58-49)30-47-40(23-25-52(61)62)37(8)43(56-47)27-46(39)55-44;/h10,15,17,19,21,27-31,51,60H,1,11-14,16,18,20,22-26H2,2-9H3,(H4,55,56,57,58,59,61,62,63,64);/q;+2/p-2/b33-17+,34-19+,35-21+,43-27-,44-29-,45-28-,46-27-,47-30-,48-30-,49-28-,50-29-;/t51-;/m0./s1
• InChIKey: PDYODZVCODUKFH-ZOMLSHGTSA-L
• SMILES:
  CACTVS 3.385: CC(C)=CCC/C(C)=C/CC/C(C)=C/CC/C(C)=C/CC[C@H](O)C1=C(C)C2=NC1=Cc3n4[Fe][N@]5C(=Cc4c(C=C)c3C)C(=C(CCC(O)=O)C5=CC6=NC(=C2)C(=C6CCC(O)=O)C=O)C
  OpenEye OEToolkits 2.0.7: Cc1c2n3c(c1C=C)C=C4C(=C(C5=CC6=[N]7[Fe]3(N45)[N]8=C(C=C7C(=C6CCC(=O)O)C=O)C(=C(C8=C2)C(CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C)O)C)CCC(=O)O)C
  OpenEye OEToolkits 2.0.7: Cc1c2n3c(c1C=C)C=C4C(=C(C5=CC6=[N]7[Fe]3(N45)[N]8=C(C=C7C(=C6CCC(=O)O)C=O)C(=C(C8=C2)[C@H](CC/C=C(\C)/CC/C=C(\C)/CC/C=C(\C)/CCC=C(C)C)O)C)CCC(=O)O)C
  CACTVS 3.385: CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCC[CH](O)C1=C(C)C2=NC1=Cc3n4[Fe][N]5C(=Cc4c(C=C)c3C)C(=C(CCC(O)=O)C5=CC6=NC(=C2)C(=C6CCC(O)=O)C=O)C
• Formula: C54 H64 Fe N4 O6
• Name: HEME-AS
• PDB chain: 2yev Chain D Residue 1016

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2yev Structural Insights Into Electron Transfer in Caa3-Type Cytochrome Oxidases.
• Resolution: 2.36 Å
• Binding residue (original residue number in PDB): W246 V253 Y254 H299 H300 I321 A322 G326 G361 I362 G364 V365 L367 S368 D373 H377 V382 H385 F386 V389 L390 R447
• Binding residue (residue number reindexed from 1): W235 V242 Y243 H288 H289 I310 A311 G315 G350 I351 G353 V354 L356 S357 D362 H366 V371 H374 F375 V378 L379 R436
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Y31 L41 F45 I49 L70 H73 N92 D103 N110 S113 F117 W139 S166 S167 G170 T177 H250 T252 Y254 A265 Q281 H299 H300 T325 K328 H385 F386 H387 G444 M445 R447
• Catalytic site (residue number reindexed from 1): Y20 L30 F34 I38 L59 H62 N81 D92 N99 S102 F106 W128 S155 S156 G159 T166 H239 T241 Y243 A254 Q270 H288 H289 T314 K317 H374 F375 H376 G433 M434 R436
• Enzyme Commision number: 7.1.1.9: cytochrome-c oxidase.

Gene Ontology

Molecular Function

• GO:0004129 cytochrome-c oxidase activity
• GO:0009055 electron transfer activity
• 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:1902600 proton transmembrane transport

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane

External links

• PDB: RCSB:2yev, PDBe:2yev, PDBj:2yev
• PDBsum: 2yev
• PubMed: 22763450
• UniProt: P98005|COX13_THET8 Cytochrome c oxidase polypeptide I+III (Gene Name=caaA)