Structure of PDB 2yev Chain D Binding Site BS02

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 1015

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): F37 F39 A40 G43 S46 I49 R50 Y66 L70 H73 G74 M77 L78 W139 Y380 F386 H387 M391 F434 R447 R448 L473
• Binding residue (residue number reindexed from 1): F26 F28 A29 G32 S35 I38 R39 Y55 L59 H62 G63 M66 L67 W128 Y369 F375 H376 M380 F423 R436 R437 L462
• 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)