Structure of PDB 3s3d Chain A Binding Site BS03

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 IDHAS
InChIInChI=1S/C54H66N4O6.Fe/c1-10-39-36(7)44-29-50-54(51(60)22-14-21-35(6)20-13-19-34(5)18-12-17-33(4)16-11-15-32(2)3)38(9)45(57-50)28-49-42(31-59)41(24-26-53(63)64)48(58-49)30-47-40(23-25-52(61)62)37(8)43(56-47)27-46(39)55-44;/h10,15,17,19,21,27-31,51,60H,1,11-14,16,18,20,22-26H2,2-9H3,(H4,55,56,57,58,59,61,62,63,64);/q;+2/p-2/b33-17+,34-19+,35-21+,43-27-,44-29-,45-28-,46-27-,47-30-,48-30-,49-28-,50-29-;/t51-;/m0./s1
InChIKeyPDYODZVCODUKFH-ZOMLSHGTSA-L
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)=CCC/C(C)=C/CC/C(C)=C/CC/C(C)=C/CC[C@H](O)C1=C(C)C2=NC1=Cc3n4[Fe][N@]5C(=Cc4c(C=C)c3C)C(=C(CCC(O)=O)C5=CC6=NC(=C2)C(=C6CCC(O)=O)C=O)C
OpenEye OEToolkits 2.0.7Cc1c2n3c(c1C=C)C=C4C(=C(C5=CC6=[N]7[Fe]3(N45)[N]8=C(C=C7C(=C6CCC(=O)O)C=O)C(=C(C8=C2)C(CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C)O)C)CCC(=O)O)C
OpenEye OEToolkits 2.0.7Cc1c2n3c(c1C=C)C=C4C(=C(C5=CC6=[N]7[Fe]3(N45)[N]8=C(C=C7C(=C6CCC(=O)O)C=O)C(=C(C8=C2)[C@H](CC/C=C(\C)/CC/C=C(\C)/CC/C=C(\C)/CCC=C(C)C)O)C)CCC(=O)O)C
CACTVS 3.385CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCC[CH](O)C1=C(C)C2=NC1=Cc3n4[Fe][N]5C(=Cc4c(C=C)c3C)C(=C(CCC(O)=O)C5=CC6=NC(=C2)C(=C6CCC(O)=O)C=O)C
FormulaC54 H64 Fe N4 O6
NameHEME-AS
ChEMBL
DrugBank
ZINC
PDB chain3s3d Chain A Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)		Y133 W229 V236 Y237 W239 L240 H282 H283 S309 A313 V350 L353 L354 F356 I357 G360 G363 N366 A367 D372 H376 V381 H384 F385 Q388 R449
Binding residue
(residue number reindexed from 1)		Y126 W222 V229 Y230 W232 L233 H275 H276 S302 A306 V343 L346 L347 F349 I350 G353 G356 N359 A360 D365 H369 V374 H377 F378 Q381 R442
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

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

[Back to BioLiP]