Structure of PDB 2qpd Chain A Binding Site BS03

Receptor Information
>2qpd Chain A (length=557) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEISRVYEAYPEKKATLYFLVLGFLALIVGSLFGPFQALNYGNVDAYPLL
KRLLPFVQSYYQGLTLHGVLNAIVFTQLFAQAIMVYLPARELNMRPNMGL
MWLSWWMAFIGLVVAALPLLANEATVLYTFYPPLKGHWAFYLGASVFVLS
TWVSIYIVLDLWRRWKAANPGKVTPLVTYMAVVFWLMWFLASLGLVLEAV
LFLLPWSFGLVEGVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQA
GGRLVSDPMARLAFLLFLLLSTPVGFHHQFADPGIDPTWKMIHSVLTLFV
AVPSLMTAFTVAASLEFAGRLRGGRGLFGWIRALPWDNPAFVAPVLGLLG
FIPGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLVTLTAMGSLYWLL
PNLTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYIAQ
VPDAYPHAAVPMVFNVLAGIVLLVALLLFIYGLFSVLLSRERKPELAEAP
LPFAEVISGPEDRRLVLAMDRIGFWFAVAAILVVLAYGPTLVQLFGHLNP
VPGWRLW
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 chain2qpd 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

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PDB2qpd An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from Thermus thermophilus.
Resolution3.25 Å
Binding residue
(original residue number in PDB)		Y133 V236 Y237 W239 L240 H282 H283 S309 A313 L353 L354 F356 G360 G363 N366 D372 H376 V381 H384 F385 Q388 V389 R449
Binding residue
(residue number reindexed from 1)		Y128 V231 Y232 W234 L235 H277 H278 S304 A308 L348 L349 F351 G355 G358 N361 D367 H371 V376 H379 F380 Q383 V384 R444
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) H67 P96 Y128 S150 T151 H228 I230 Y232 Y243 H277 H278 S304 G326 H379 F380 H381 R444 R445
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2qpd, PDBe:2qpd, PDBj:2qpd
PDBsum2qpd
PubMed18084085
UniProtQ5SJ79|COX1_THET8 Cytochrome c oxidase subunit 1 (Gene Name=cbaA)

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