Structure of PDB 5djq Chain K Binding Site BS03

Receptor Information
>5djq Chain K (length=465) Species: 316 (Stutzerimonas stutzeri) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
STAYSYKVVRQFAIMTVVWGIVGMGLGVFIAAQLAWPFLNFDLPWTSFGR
LRPLHTNAVIFAFGGCALFATSYYSVQRTCQTTLFAPKLAAFTFWGWQLV
ILLAAISLPLGFTSSKEYAELEWPIDILITIVWVAYAVVFFGTLAKRKVK
HIYVGNWFFGAFILTVAILHVVNNLEIPVTAMKSYSLYAGATDAMVQWWY
GHNAVGFFLTAGFLGIMYYFVPKQAERPVYSYRLSIVHFWALITVYIWAG
PHHLHYTALPDWAQSLGMVMSLILLAPSWGGMINGMMTLSGAWHKLRSDP
ILRFLVVSLAFYGMSTFEGPMMAIKTVNALSHYTDWTIGHVHAGALGWVA
MVSIGALYHLVPKVFGREQMHSIGLINTHFWLATIGTVLYIASMWVNGIA
QGLMWRAINDDGTLTYSFVESLEASHPGFVVRMIGGAIFFAGMLVMAYNT
WRTVQAAKPAEYDAA
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 chain5djq Chain K Residue 502 [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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PDB5djq 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 L39 R57 H60 T61 V64 I65 Y123 I343 V346 H347 A350 L351 Y395 R437 G441
Binding residue
(residue number reindexed from 1)		M24 G27 V28 I30 A31 L34 R52 H55 T56 V59 I60 Y118 I338 V341 H342 A345 L346 Y390 R432 G436
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5djq, PDBe:5djq, PDBj:5djq
PDBsum5djq
PubMed20576851
UniProtD9IA43|CCON1_STUST Cbb3-type cytochrome c oxidase subunit CcoN1 (Gene Name=ccoN1)

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