Structure of PDB 3qjr Chain A Binding Site BS03

Receptor Information

>3qjr Chain A (length=552) Species: 300852 (Thermus thermophilus HB8)

VYEAYPEKKATLYFLVLGFLALIVGSLFGPFQALNYGNVDAYPLLKRLLP
FVQSYYQGLTLHGVLNAIVFTQLFAQAIMVYLPARELNMRPNMGLMWLSW
WMAFIGLVVAALPLLANEATVLYTFYPPLKGHWAFYLGASVFVLSTWVSI
YIVLDLWRRWKAANPGKVTPLVTYMAVVFWLMWFLASLGLVLEAVLFLLP
WSFGLVEGVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQAGGKLV
SDPMARLAFLLFLLLSTPVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSL
MTAFTVAASLEFAGRLRGGRGLFGWIRALPWDNPAFVAPVLGLLGFIPGG
AGGIVNASFTLDYVVHNTAWVPGHFHLQVASLVTLTAMGSLYWLLPNLTG
KPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYIAQVPDAY
PHAAVPMVFNVLAGIVLLVALLLFIYGLFSVLLSRERKPELAEAPLPFAE
VISGPEDRRLVLAMDRIGFWFAVAAILVVLAYGPTLVQLFGHLNPVPGWR
LW

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: 3qjr Chain A Residue 801

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3qjr Structural changes that occur upon photolysis of the Fe(II)(a3)-CO complex in the cytochrome ba(3)-oxidase of Thermus thermophilus: A combined X-ray crystallographic and infrared spectral study demonstrates CO binding to Cu(B).
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): Y133 W229 V236 H282 H283 S309 A313 L353 F356 G360 G363 N366 A367 D372 H376 V381 H384 F385 Q388 V389 R449
• Binding residue (residue number reindexed from 1): Y123 W219 V226 H272 H273 S299 A303 L343 F346 G350 G353 N356 A357 D362 H366 V371 H374 F375 Q378 V379 R439
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H72 P101 Y133 S155 T156 H233 I235 Y237 Y248 H282 H283 S309 G331 H384 F385 H386 R449 R450
• Catalytic site (residue number reindexed from 1): H62 P91 Y123 S145 T146 H223 I225 Y227 Y238 H272 H273 S299 G321 H374 F375 H376 R439 R440
• 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:0009060 aerobic respiration
• GO:1902600 proton transmembrane transport

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane

External links

• PDB: RCSB:3qjr, PDBe:3qjr, PDBj:3qjr
• PDBsum: 3qjr
• PubMed: 22226917
• UniProt: Q5SJ79|COX1_THET8 Cytochrome c oxidase subunit 1 (Gene Name=cbaA)