Structure of PDB 3s3d Chain A Binding Site BS02

Receptor Information
>3s3d Chain A (length=555) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ISRVYEAYPEKKATLYFLVLGFLALIVGSLFGPFQALNYGNVDAYPLLKR
LLPFVQSYYQGLTLHGVLNAIVFTQLFAQAIMVYLPARELNMRPNMGLMW
LSWWMAFIGLVVAALPLLANEATVLYTFYPPLKGHWAFYLGASVFVLSTW
VSIYIVLDLWRRWKAANPGKVTPLVTYMAVVFWLMWFLASLGLVLEAVLF
LLPWSFGLVEGVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQAGG
KLVSDPMARLAFLLFLLLSTPVGFHHQFADPGIDPTWKMIHSVLTLFVAV
PSLMTAFTVAASLEFAGRLRGGRGLFGWIRALPWDNPAFVAPVLGLLGFI
PGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLVTLTAMGSLYWLLPN
LTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYIAQVP
DAYPHAAVPMVFNVLAGIVLLVALLLFIYGLFSVLLSRERKPELAEAPLP
FAEVISGPEDRRLVLAMDRIGFWFAVAAILVVLAYGPTLVQLFGHLNPVP
GWRLW
Ligand information
Ligand IDHEM
InChIInChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
InChIKeyKABFMIBPWCXCRK-RGGAHWMASA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
CACTVS 3.385CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C
ACDLabs 12.01C=1c3c(c(c4C=C5C(=C(C=6C=C7C(=C(C8=CC=2C(=C(C=1N=2[Fe](n34)(N5=6)N78)CCC(=O)O)C)\C=C)C)\C=C)C)C)CCC(=O)O
FormulaC34 H32 Fe N4 O4
NamePROTOPORPHYRIN IX CONTAINING FE;
HEME
ChEMBL
DrugBankDB18267
ZINC
PDB chain3s3d Chain A Residue 800 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3s3d Mobility of Xe atoms within the oxygen diffusion channel of cytochrome ba(3) oxidase.
Resolution3.75 Å
Binding residue
(original residue number in PDB)		G39 P40 Q42 Y46 Y65 L69 H72 N76 Y133 F385 H386 A390 T394 M432 M435 R450
Binding residue
(residue number reindexed from 1)		G32 P33 Q35 Y39 Y58 L62 H65 N69 Y126 F378 H379 A383 T387 M425 M428 R443
Annotation score1
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) H65 P94 Y126 S148 T149 H226 I228 Y230 Y241 H275 H276 S302 G324 H377 F378 H379 R442 R443
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3s3d, PDBe:3s3d, PDBj:3s3d
PDBsum3s3d
PubMed22607023
UniProtQ5SJ79|COX1_THET8 Cytochrome c oxidase subunit 1 (Gene Name=cbaA)

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