Structure of PDB 2qpd Chain A Binding Site BS02

Receptor Information
>2qpd Chain A (length=557) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEISRVYEAYPEKKATLYFLVLGFLALIVGSLFGPFQALNYGNVDAYPLL
KRLLPFVQSYYQGLTLHGVLNAIVFTQLFAQAIMVYLPARELNMRPNMGL
MWLSWWMAFIGLVVAALPLLANEATVLYTFYPPLKGHWAFYLGASVFVLS
TWVSIYIVLDLWRRWKAANPGKVTPLVTYMAVVFWLMWFLASLGLVLEAV
LFLLPWSFGLVEGVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQA
GGRLVSDPMARLAFLLFLLLSTPVGFHHQFADPGIDPTWKMIHSVLTLFV
AVPSLMTAFTVAASLEFAGRLRGGRGLFGWIRALPWDNPAFVAPVLGLLG
FIPGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLVTLTAMGSLYWLL
PNLTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYIAQ
VPDAYPHAAVPMVFNVLAGIVLLVALLLFIYGLFSVLLSRERKPELAEAP
LPFAEVISGPEDRRLVLAMDRIGFWFAVAAILVVLAYGPTLVQLFGHLNP
VPGWRLW
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 chain2qpd 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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PDB2qpd An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from Thermus thermophilus.
Resolution3.25 Å
Binding residue
(original residue number in PDB)		G39 P40 Q42 A43 Y46 Y65 L69 H72 N76 Y133 F385 H386 V389 A390 M435 R450
Binding residue
(residue number reindexed from 1)		G34 P35 Q37 A38 Y41 Y60 L64 H67 N71 Y128 F380 H381 V384 A385 M430 R445
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) H67 P96 Y128 S150 T151 H228 I230 Y232 Y243 H277 H278 S304 G326 H379 F380 H381 R444 R445
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:2qpd, PDBe:2qpd, PDBj:2qpd
PDBsum2qpd
PubMed18084085
UniProtQ5SJ79|COX1_THET8 Cytochrome c oxidase subunit 1 (Gene Name=cbaA)

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