Structure of PDB 3s3a Chain A Binding Site BS03

Receptor Information
>3s3a Chain A (length=554) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SRVYEAYPEKKATLYFLVLGFLALIVGSLFGPFQALNYGNVDAYPLLKRL
LPFVQSYYQGLTLHGVLNAIVFTQLFAQAIMVYLPARELNMRPNMGLMWL
SWWMAFIGLVVAALPLLANEATVLYTFYPPLKGHWAFYLGASVFVLSTWV
SIYIVLDLWRRWKAANPGKVTPLVTYMAVVFWLMWFLASLGLVLEAVLFL
LPWSFGLVEGVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQAGGK
LVSDPMARLAFLLFLLLSTPVGFHHQFADPGIDPTWKMIHSVLTLFVAVP
SLMTAFTVAASLEFAGRLRGGRGLFGWIRALPWDNPAFVAPVLGLLGFIP
GGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLVTLTAMGSLYWLLPNL
TGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYIAQVPD
AYPHAAVPMVFNVLAGIVLLVALLLFIYGLFSVLLSRERKPELAEAPLPF
AEVISGPEDRRLVLAMDRIGFWFAVAAILVVLAYGPTLVQLFGHLNPVPG
WRLW
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 chain3s3a Chain A Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3s3a Mobility of Xe atoms within the oxygen diffusion channel of cytochrome ba(3) oxidase.
Resolution4.25 Å
Binding residue
(original residue number in PDB)		Y133 W229 V236 Y237 W239 H282 S309 A313 V350 L353 L354 F356 G360 N366 A367 D372 H376 V381 H384 F385 Q388 V389 R449
Binding residue
(residue number reindexed from 1)		Y125 W221 V228 Y229 W231 H274 S301 A305 V342 L345 L346 F348 G352 N358 A359 D364 H368 V373 H376 F377 Q380 V381 R441
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) H64 P93 Y125 S147 T148 H225 I227 Y229 Y240 H274 H275 S301 G323 H376 F377 H378 R441 R442
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
View graph for
Cellular Component
External links
PDB RCSB:3s3a, PDBe:3s3a, PDBj:3s3a
PDBsum3s3a
PubMed22607023
UniProtQ5SJ79|COX1_THET8 Cytochrome c oxidase subunit 1 (Gene Name=cbaA)

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