Structure of PDB 3din Chain B Binding Site BS02

Receptor Information
>3din Chain B (length=816) Species: 243274 (Thermotoga maritima MSB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MILFDKNKRILKKYAKMVSKINQIESDLRSKKNSELIRLSMVLKEKVNSF
EDADEHLFEAFALVREAARRTLGMRPFDVQVMGGIALHEGKVAEMKTGEG
KTLAATMPIYLNALIGKGVHLVTVNDYLARRDALWMGPVYLFLGLRVGVI
NSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAF
QVELKEITRKEAYLCDVTYGTNNEFGFDYLRDNLVLDYNDKVQRGHFYAI
VDEADSVLIDEARTPLIISGPSKESPSVYRRFAQIAKKFVKDKDFTVDEK
ARTIILTEEGVAKAEKIIGVENLYDPGNVSLLYHLINALKALHLFKKDVD
YVVMNGEVIIVDEFTGRLLPGRRYSGGLHQAIEAKEGVPIKEESITYATI
TFQNYFRMYEKLAGMTGTAKTEESEFVQVYGMEVVVIPTHKPMIRKDHDD
LVFRTQKEKYEKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIP
HQVLNAKYHEKEAEIVAKAGQKGMVTIATNMAGRGTDIKLGPGVAELGGL
CIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLEDDLLRIFGSEQIG
KVMNILKIEEGQPIQHPMLSKLIENIQKKVEGINFSIRKTLMEMDDVLDK
QRRAVYSLRDQILLEKDYDEYLKDIFEDVVSTRVEEFCSGKNWDIESLKN
SLSFFPAGLFDLDEKQFSSSEELHDYLFNRLWEEYQRKKQEIGEDYRKVI
RFLMLRIIDDHWRRYLEEVEHVKEAVQLRSYGQKDPIVEFKKETYYMFDE
MMRRINDTIANYVLRV
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain3din Chain B Residue 873 [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]
PDB3din Structure of a complex of the ATPase SecA and the protein-translocation channel.
Resolution4.5 Å
Binding residue
(original residue number in PDB)		M74 R75 P76 K96 G98 G100 K101 T102 L103 L187 R573 Q574
Binding residue
(residue number reindexed from 1)		M74 R75 P76 K96 G98 G100 K101 T102 L103 L187 R573 Q574
Annotation score4
Enzymatic activity
Enzyme Commision number 7.4.2.8: protein-secreting ATPase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0008564 protein-exporting ATPase activity
Biological Process
GO:0006605 protein targeting
GO:0006886 intracellular protein transport
GO:0015031 protein transport
GO:0017038 protein import
GO:0043952 protein transport by the Sec complex
GO:0065002 intracellular protein transmembrane transport
Cellular Component
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0031522 cell envelope Sec protein transport complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3din, PDBe:3din, PDBj:3din
PDBsum3din
PubMed18923516
UniProtQ9X1R4|SECA_THEMA Protein translocase subunit SecA (Gene Name=secA)

[Back to BioLiP]