Structure of PDB 3oma Chain A Binding Site BS03

Receptor Information

>3oma Chain A (length=535) Species: 272943 (Cereibacter sphaeroides 2.4.1)

FTRWFMSTNHKDIGVLYLFTGGLVGLISVAFTVYMRMELMAPGVQFMCAE
HLESGLVKGFFQSLWPSAVENCTPNGHLWNVMITGHGILMMFFVVIPALF
GGFGNYFMPLHIGAPDMAFPRMNNLSYWLYVAGTSLAVASLFAPGGNGQL
GSGIGWVLYPPLSTSESGYSTDLAIFAVHLSGASSILGAINMITTFLNMR
APGMTMHKVPLFAWSIFVTAWLILLALPVLAGAITMLLTDRNFGTTFFQP
SGGGDPVLYQHILWFFGHPEVYIIVLPAFGIVSHVIATFAKKPIFGYLPM
VYAMVAIGVLGFVVWAHHMYTAGLSLTQQSYFMMATMVIAVPTGIMIFSW
IATMWGGSIELKTPMLWALGFLFLFTVGGVTGIVLSQASVDRYYHDTYYV
VAHFHYVMSLGAVFGIFAGIYFWIGKMSGRQYPEWAGKLHFWMMFVGANL
TFFPQHFLGRQGMPRRYIDYPEAFATWNFVSSLGAFLSFASFLFFLGVIF
YTLTRGARVTANNYWNEHADTLEWTLTSPPPEHTF

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: 3oma Chain A Residue 2

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3oma Crystallographic and online spectral evidence for role of conformational change and conserved water in cytochrome oxidase proton pump.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): W172 W280 V287 Y288 H333 H334 G360 G395 G398 I399 L401 S402 D407 H411 H419 F420 V423 M424 R481
• Binding residue (residue number reindexed from 1): W156 W264 V271 Y272 H317 H318 G344 G379 G382 I383 L385 S386 D391 H395 H403 F404 V407 M408 R465
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Y33 I43 F47 M51 I99 H102 N121 D132 N139 S142 Y146 W172 S200 S201 G204 T211 H284 E286 Y288 S299 P315 H333 H334 T359 M362 H419 F420 H421 R481
• Catalytic site (residue number reindexed from 1): Y17 I27 F31 M35 I83 H86 N105 D116 N123 S126 Y130 W156 S184 S185 G188 T195 H268 E270 Y272 S283 P299 H317 H318 T343 M346 H403 F404 H405 R465
• Enzyme Commision number: 7.1.1.9: cytochrome-c oxidase.

Gene Ontology

Molecular Function

• GO:0004129 cytochrome-c oxidase activity
• GO:0016491 oxidoreductase 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

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0045277 respiratory chain complex IV

External links

• PDB: RCSB:3oma, PDBe:3oma, PDBj:3oma
• PDBsum: 3oma
• PubMed: 21205904
• UniProt: Q3J5A7