Structure of PDB 2ibm Chain A Binding Site BS01

Receptor Information
>2ibm Chain A (length=780) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLGILNKMFDPTKRTLNRYEKIANDIDAIRGDYENLSDDALKHKTIEFKE
RLEKGATTDDLLVEAFAVVREASRRVTGMFPFKVQLMGGVALHDGNIAEM
KTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIFEFLGL
TVGLNLNSMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRP
LHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAFVRTLKAEKDY
TYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAM
QKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESM
TLATITFQNYFRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIPTNRPVVR
DDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLK
NKGIPHQVLNAKNHEREAQIIEEAGQKGAVTIATNMAGRGTDIKLGEGVK
ELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDELMRRFG
AERTMAMLDRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQLLQYD
DVLRQQREVIYKQRFEVIDSENLREIVENMIKSSLERAIAAYTPREELPE
EWKLDGLVDLINTTYLDEGALEKSDIFGKEPDEMLELIMDRIITKYNEKE
EQFGKEQMREFEKVIVLRAVDSKWMDHIDAMDQLRQGIHLRAYAQTNPLR
EYQMEGFAMFEHMIESIEDEVAKFVMKAEI
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 chain2ibm Chain A Residue 781 [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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PDB2ibm A Novel Dimer Interface and Conformational Changes Revealed by an X-ray Structure of B. subtilis SecA.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		M79 F82 Q85 G103 E104 G105 K106 T107 D492
Binding residue
(residue number reindexed from 1)		M79 F82 Q85 G103 E104 G105 K106 T107 D492
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
GO:0046872 metal ion binding
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
GO:0045121 membrane raft

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2ibm, PDBe:2ibm, PDBj:2ibm
PDBsum2ibm
PubMed16989859
UniProtP28366|SECA_BACSU Protein translocase subunit SecA (Gene Name=secA)

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