Structure of PDB 2dys Chain N Binding Site BS10

Receptor Information

>2dys Chain N (length=514) Species: 9913 (Bos taurus)

MFINRWLFSTNHKDIGTLYLLFGAWAGMVGTALSLLIRAELGQPGTLLGD
DQIYNVVVTAHAFVMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRMNNM
SFWLLPPSFLLLLASSMVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFSL
HLAGVSSILGAINFITTIINMKPPAMSQYQTPLFVWSVMITAVLLLLSLP
VLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPG
FGMISHIVTYYSGKKEPFGYMGMVWAMMSIGFLGFIVWAHHMFTVGMDVD
TRAYFTSATMIIAIPTGVKVFSWLATLHGGNIKWSPAMMWALGFIFLFTV
GGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFVHWFPLF
SGYTLNDTWAKIHFAIMFVGVNMTFFPQHFLGLSGMPRRYSDYPDAYTMW
NTISSMGSFISLTAVMLMVFIIWEAFASKREVLTVDLTTTNLEWLNGCPP
PYHTFEEPTYVNLK

Ligand information

• Ligand ID: PEK
• InChI: InChI=1S/C43H78NO8P/c1-3-5-7-9-11-13-15-17-19-20-22-24-26-28-30-32-34-36-43(46)52-41(40-51-53(47,48)50-38-37-44)39-49-42(45)35-33-31-29-27-25-23-21-18-16-14-12-10-8-6-4-2/h11,13,17,19,22,24,28,30,41H,3-10,12,14-16,18,20-21,23,25-27,29,31-40,44H2,1-2H3,(H,47,48)/b13-11-,19-17-,24-22-,30-28-/t41-/m1/s1
• InChIKey: ANRKEHNWXKCXDB-BHFWLYLHSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCCN)OC(=O)CCC\C=C/C\C=C/C\C=C/C\C=C/CCCCC
  CACTVS 3.341: CCCCCCCCCCCCCCCCCC(=O)OC[CH](CO[P](O)(=O)OCCN)OC(=O)CCCC=CCC=CCC=CCC=CCCCCC
  ACDLabs 10.04: O=C(OCC(OC(=O)CCC\C=C/C\C=C/C\C=C/C\C=C/CCCCC)COP(=O)(OCCN)O)CCCCCCCCCCCCCCCCC
  CACTVS 3.341: CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](O)(=O)OCCN)OC(=O)CCC\C=C/C/C=C\C\C=C/C/C=C\CCCCC
  OpenEye OEToolkits 1.5.0: CCCCCCCCCCCCCCCCCC(=O)OCC(COP(=O)(O)OCCN)OC(=O)CCCC=CCC=CCC=CCC=CCCCCC
• Formula: C43 H78 N O8 P
• Name: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE;
  PHOSPHATIDYLETHANOLAMINE;
  2-ARACHIDONOYL-1-STEAROYL-SN-GLYCEROL-3-PHOSPHOETHANOLAMINE
• ZINC: ZINC000085581337
• PDB chain: 2dys Chain P Residue 305

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2dys Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): H151 L215
• Binding residue (residue number reindexed from 1): H151 L215
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Y19 V29 L33 I37 V58 H61 N80 D91 N98 S101 L105 W126 S156 S157 G160 T167 H240 E242 Y244 S255 G272 H290 H291 T316 K319 H376 F377 H378 R438 R439
• Catalytic site (residue number reindexed from 1): Y19 V29 L33 I37 V58 H61 N80 D91 N98 S101 L105 W126 S156 S157 G160 T167 H240 E242 Y244 S255 G272 H290 H291 T316 K319 H376 F377 H378 R438 R439
• Enzyme Commision number: 7.1.1.9: cytochrome-c oxidase.

Gene Ontology

Molecular Function

• GO:0004129 cytochrome-c oxidase activity
• 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

Cellular Component

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

External links

• PDB: RCSB:2dys, PDBe:2dys, PDBj:2dys
• PDBsum: 2dys
• PubMed: 17332748
• UniProt: P00396|COX1_BOVIN Cytochrome c oxidase subunit 1 (Gene Name=MT-CO1)