Structure of PDB 8tso Chain A Binding Site BS02

Receptor Information
>8tso Chain A (length=573) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LSTWQTFRRLWPTIAPFKAGLIVAGVALILNAASDTFMLSLLKPLLDDGF
GKTDRSVLVWMPLVVIGLMILRGITSYVSSYCISWVSGKVVMTMRRRLFG
HMMGMPVSFFDKQSTGTLLSRITYDSEQVASSSSGALITVVREGASIIGL
FIMMFYYSWQLSIILIVLAPIVSIAIRVVSKRFRNISKNMQNTMGQVTTS
AEQMLKGHKEVLIFGGQEVETKRFDKVSNRMRLQGMKMVSASSISDPIIQ
LIASLALAFVLYAASFPSVMDSLTAGTITVVFSSMIALMRPLKSLTNVNA
QFQRGMAACQTLFTILDSEQEKDEGKRVIERATGDVEFRNVTFTYPGRDV
PALRNINLKIPAGKTVALVGRSGSGKSTIASLITRFYDIDEGEILMDGHD
LREYTLASLRNQVALVSQNVHLFNDTVANNIAYARTEQYSREQIEEAARM
AYAMDFINKMDNGLDTVIGENGVLLSGGQRQRIAIARALLRDSPILILDE
ATSALDTESERAIQAALDELQKNRTSLVIAHRLSTIEKADEIVVVEDGVI
VERGTHNDLLEHRGVYAQLHKMQ
Ligand information
Ligand IDKDL
InChIInChI=1S/C110H202N2O39P2/c1-7-13-19-25-31-37-38-44-50-56-62-68-92(123)142-82(66-60-54-48-42-35-29-23-17-11-5)72-94(125)146-104-96(112-90(121)71-81(65-59-53-47-41-34-28-22-16-10-4)141-91(122)67-61-55-49-43-36-30-24-18-12-6)105(144-88(102(104)150-152(133,134)135)78-140-109(107(129)130)74-86(98(127)101(148-109)85(119)76-114)147-110(108(131)132)73-83(117)97(126)100(149-110)84(118)75-113)139-77-87-99(128)103(145-93(124)70-80(116)64-58-52-46-40-33-27-21-15-9-3)95(106(143-87)151-153(136,137)138)111-89(120)69-79(115)63-57-51-45-39-32-26-20-14-8-2/h79-88,95-106,113-119,126-128H,7-78H2,1-6H3,(H,111,120)(H,112,121)(H,129,130)(H,131,132)(H2,133,134,135)(H2,136,137,138)/t79-,80-,81-,82-,83-,84-,85-,86-,87-,88-,95-,96-,97-,98-,99-,100-,101-,102-,103-,104-,105-,106-,109-,110-/m1/s1
InChIKeyDIXUKJUHGLIZGU-OIPVZEHTSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCCCCCCCCCC(=O)O[CH](CCCCCCCCCCC)CC(=O)O[CH]1[CH](NC(=O)C[CH](CCCCCCCCCCC)OC(=O)CCCCCCCCCCC)[CH](OC[CH]2O[CH](O[P](O)(O)=O)[CH](NC(=O)C[CH](O)CCCCCCCCCCC)[CH](OC(=O)C[CH](O)CCCCCCCCCCC)[CH]2O)O[CH](CO[C]3(C[CH](O[C]4(C[CH](O)[CH](O)[CH](O4)[CH](O)CO)C(O)=O)[CH](O)[CH](O3)[CH](O)CO)C(O)=O)[CH]1O[P](O)(O)=O
OpenEye OEToolkits 2.0.7CCCCCCCCCCCCCC(=O)OC(CCCCCCCCCCC)CC(=O)OC1C(C(OC(C1OP(=O)(O)O)COC2(CC(C(C(O2)C(CO)O)O)OC3(CC(C(C(O3)C(CO)O)O)O)C(=O)O)C(=O)O)OCC4C(C(C(C(O4)OP(=O)(O)O)NC(=O)CC(CCCCCCCCCCC)O)OC(=O)CC(CCCCCCCCCCC)O)O)NC(=O)CC(CCCCCCCCCCC)OC(=O)CCCCCCCCCCC
OpenEye OEToolkits 2.0.7CCCCCCCCCCCCCC(=O)O[C@H](CCCCCCCCCCC)CC(=O)O[C@@H]1[C@H]([C@@H](O[C@@H]([C@H]1OP(=O)(O)O)CO[C@@]2(C[C@H]([C@H]([C@H](O2)[C@@H](CO)O)O)O[C@@]3(C[C@H]([C@H]([C@H](O3)[C@@H](CO)O)O)O)C(=O)O)C(=O)O)OC[C@@H]4[C@H]([C@@H]([C@H]([C@H](O4)OP(=O)(O)O)NC(=O)C[C@@H](CCCCCCCCCCC)O)OC(=O)C[C@@H](CCCCCCCCCCC)O)O)NC(=O)C[C@@H](CCCCCCCCCCC)OC(=O)CCCCCCCCCCC
CACTVS 3.385CCCCCCCCCCCCCC(=O)O[C@H](CCCCCCCCCCC)CC(=O)O[C@@H]1[C@@H](NC(=O)C[C@@H](CCCCCCCCCCC)OC(=O)CCCCCCCCCCC)[C@H](OC[C@H]2O[C@H](O[P](O)(O)=O)[C@H](NC(=O)C[C@H](O)CCCCCCCCCCC)[C@@H](OC(=O)C[C@H](O)CCCCCCCCCCC)[C@@H]2O)O[C@H](CO[C@@]3(C[C@@H](O[C@@]4(C[C@@H](O)[C@@H](O)[C@H](O4)[C@H](O)CO)C(O)=O)[C@@H](O)[C@H](O3)[C@H](O)CO)C(O)=O)[C@H]1O[P](O)(O)=O
FormulaC110 H202 N2 O39 P2
Name(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]-5-oxidanyl-oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain8tso Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8tso Native mass spectrometry captures snapshots of the MsbA transport cycle
Resolution2.68 Å
Binding residue
(original residue number in PDB)
V29 Y83 Y87 C88 W91
Binding residue
(residue number reindexed from 1)
V23 Y77 Y81 C82 W85
Annotation score1
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0008289 lipid binding
GO:0008559 ABC-type xenobiotic transporter activity
GO:0015437 lipopolysaccharide floppase activity
GO:0034040 ATPase-coupled lipid transmembrane transporter activity
GO:0042802 identical protein binding
Biological Process
GO:0006869 lipid transport
GO:0015920 lipopolysaccharide transport
GO:0034204 lipid translocation
GO:0042908 xenobiotic transport
GO:0055085 transmembrane transport
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0043190 ATP-binding cassette (ABC) transporter complex
GO:1990199 MsbA transporter complex

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:8tso, PDBe:8tso, PDBj:8tso
PDBsum8tso
PubMed
UniProtP60752|MSBA_ECOLI ATP-dependent lipid A-core flippase (Gene Name=msbA)

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