Structure of PDB 3mk7 Chain A Binding Site BS02

Receptor Information
>3mk7 Chain A (length=466) Species: 316 (Stutzerimonas stutzeri) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TSTAYSYKVVRQFAIMTVVWGIVGMGLGVFIAAQLAWPFLNFDLPWTSFG
RLRPLHTNAVIFAFGGCALFATSYYSVQRTCQTTLFAPKLAAFTFWGWQL
VILLAAISLPLGFTSSKEYAELEWPIDILITIVWVAYAVVFFGTLAKRKV
KHIYVGNWFFGAFILTVAILHVVNNLEIPVTAMKSYSLYAGATDAMVQWW
YGHNAVGFFLTAGFLGIMYYFVPKQAERPVYSYRLSIVHFWALITVYIWA
GPHHLHYTALPDWAQSLGMVMSLILLAPSWGGMINGMMTLSGAWHKLRSD
PILRFLVVSLAFYGMSTFEGPMMAIKTVNALSHYTDWTIGHVHAGALGWV
AMVSIGALYHLVPKVFGREQMHSIGLINTHFWLATIGTVLYIASMWVNGI
AQGLMWRAINDDGTLTYSFVESLEASHPGFVVRMIGGAIFFAGMLVMAYN
TWRTVQAAKPAEYDAA
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 chain3mk7 Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3mk7 The Structure of cbb3 Cytochrome Oxidase Provides Insights into Proton Pumping
Resolution3.2 Å
Binding residue
(original residue number in PDB)		M29 G32 V33 I35 A36 R57 H60 V64 Y123 I343 V346 H347 A350 L351 Y395 G441
Binding residue
(residue number reindexed from 1)		M25 G28 V29 I31 A32 R53 H56 V60 Y119 I339 V342 H343 A346 L347 Y391 G437
Annotation score1
Enzymatic activity
Enzyme Commision number 7.1.1.9: cytochrome-c oxidase.
Gene Ontology
Molecular Function
GO:0004129 cytochrome-c oxidase activity
GO:0005506 iron ion binding
GO:0005507 copper ion binding
GO:0008121 ubiquinol-cytochrome-c reductase activity
GO:0015078 proton transmembrane transporter activity
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0019825 oxygen binding
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:0019411 aerobic respiration, using ferrous ions as electron donor
GO:0019646 aerobic electron transport chain
GO:0022904 respiratory electron transport chain
GO:1902600 proton transmembrane transport
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0070069 cytochrome complex
GO:0098803 respiratory chain complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3mk7, PDBe:3mk7, PDBj:3mk7
PDBsum3mk7
PubMed20576851
UniProtD9IA43|CCON1_STUST Cbb3-type cytochrome c oxidase subunit CcoN1 (Gene Name=ccoN1)

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