Structure of PDB 8gym Chain C1 Binding Site BS02

Receptor Information
>8gym Chain C1 (length=674) Species: 312017 (Tetrahymena thermophila SB210) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VSVNNYFYYLDRIKKLFTYLNDLRKHILKKYVYTINHKRIAINYLYFSMV
TGLSGAALATMIRLELAHPGSPFFKGDSLRYLQVVTAHGLIMVFFVVVPI
LFGGFANFLIPYHVGSKDVAYPRLNSIGFWIQPCGYILLAKIGFLRPQFW
RYYDKTSFSFPFLEKMKYNQYKEYKNDYLFYLDFLKKEITDDHSFFWKAR
KVIKLPQYSVFSFVPLKLMMWKTMINYPESFWYAASRVVQSRRKKVFVTK
CSARTLTTAGWTFITPFSSNIKYTGVGSQDILILSVVFAGISTTISFTNL
LITRRTLAMPGLRHRRVLMPFVTISIFLTLRMLATITPVLGAAVIMMAFD
RHWQTTFFEYAYGGDPILSQHLFWFFGHPEVYVLIIPTFGFINMIVPHNN
TRRVASKHHMIWAIYVMAYMGYLVWGHHMYLVGLDHRSRTMYSTITIMIS
MPATIKVVNWTLSLVNGALKIDLPFLFSMSFLLLFLVAGFTGMWLSHVSL
NVSMHDTFYVVAHFHIMLSGAAMTGIFSGIYYYFNALFGVKYSRMFGYMH
LIYYSGGQWVAFVPLFYLGFSGMPRRIHDYPVVFMGWHSMSTTGHFITLV
GIIFFFLMMFDSHIERRASTSTTLGLPRWYKRISYYIFKIRYLQHTKSKM
NGIPGSTVRLMLINRHFVEYEVYE
Ligand information
Ligand IDHEA
InChIInChI=1S/C49H58N4O6.Fe/c1-9-34-31(6)39-25-45-49(46(55)18-12-17-30(5)16-11-15-29(4)14-10-13-28(2)3)33(8)40(52-45)24-44-37(27-54)36(20-22-48(58)59)43(53-44)26-42-35(19-21-47(56)57)32(7)38(51-42)23-41(34)50-39;/h9,13,15,17,23-27,46,55H,1,10-12,14,16,18-22H2,2-8H3,(H4,50,51,52,53,54,56,57,58,59);/q;+2/p-2/b29-15+,30-17+,38-23-,39-25-,40-24-,41-23-,42-26-,43-26-,44-24-,45-25-;/t46-;/m0./s1
InChIKeyZGGYGTCPXNDTRV-PRYGPKJJSA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2Cc1c2n3c(c1C=C)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C=O)CCC(=O)O)C(=C(C7=C2)[C@H](CC/C=C(\C)/CC/C=C(\C)/CCC=C(C)C)O)C)CCC(=O)O)C
CACTVS 3.370CC(C)=CCC/C(C)=C/CC/C(C)=C/CC[C@H](O)C1=C(C)C2=N3|[Fe]45|N6=C(C=c7n4c(=C2)c(C=O)c7CCC(O)=O)C(=C(C)C6=Cc8n5c(C=C13)c(C)c8C=C)CCC(O)=O
CACTVS 3.370CC(C)=CCCC(C)=CCCC(C)=CCC[CH](O)C1=C(C)C2=N3|[Fe]45|N6=C(C=c7n4c(=C2)c(C=O)c7CCC(O)=O)C(=C(C)C6=Cc8n5c(C=C13)c(C)c8C=C)CCC(O)=O
OpenEye OEToolkits 1.7.2Cc1c2n3c(c1C=C)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C=O)CCC(=O)O)C(=C(C7=C2)C(CCC=C(C)CCC=C(C)CCC=C(C)C)O)C)CCC(=O)O)C
ACDLabs 12.01O=C(O)CCC1=C(C2=Cc4c(c(c3C=C5C(=C(C=6C=C7C(C=O)=C(C8=CC1=N2[Fe](n34)(N5=6)N78)CCC(=O)O)C)C(O)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)C)C)/C=C)C
FormulaC49 H56 Fe N4 O6
NameHEME-A
ChEMBL
DrugBank
ZINC
PDB chain8gym Chain C1 Residue 703 [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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PDB8gym Structures of Tetrahymena thermophila respiratory megacomplexes on the tubular mitochondrial cristae.
Resolution2.96 Å
Binding residue
(original residue number in PDB)		W274 W387 V394 I398 H440 H441 A466 G502 F503 G505 M506 L508 S509 N514 H518 V523 H526 F527 M530 L531 R588
Binding residue
(residue number reindexed from 1)		W261 W374 V381 I385 H427 H428 A453 G489 F490 G492 M493 L495 S496 N501 H505 V510 H513 F514 M517 L518 R575
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:0016491 oxidoreductase activity
GO:0020037 heme binding
GO:0046872 metal ion binding
Biological Process
GO:0006119 oxidative phosphorylation
GO:0006123 mitochondrial electron transport, cytochrome c to oxygen
GO:0009060 aerobic respiration
GO:0015990 electron transport coupled proton transport
Cellular Component
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8gym, PDBe:8gym, PDBj:8gym
PDBsum8gym
PubMed37248254
UniProtQ950Y4

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