Structure of PDB 6t4h Chain A Binding Site BS01

Receptor Information
>6t4h Chain A (length=771) Species: 272563 (Clostridioides difficile 630) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ADEQEIKKLNVIVDKIDALEDSMKNLSYEELKDMTAIFKNRLKKGETLDD
ILPEAFAVVREVSKRKLGMRQYRVQLIGGIVIHQGKIAEMKTGEGKTLVE
VAPVYLNALTGKGVHVITVNDYLAERDKELMSPVYESLGMTVGVIISNQD
PNIRKQQYKCDITYGTNSEFGFDYLRDNMVPDLSHKVQRELNFAIVDEVD
SILIDEARTPLIIAGDGDEDLKLYELANSFVKTVKEEDFELDRKDKTIAL
TASGISKAESFFGITNLTDIKNIELYHHINQALRGHKLMEKDVDYVISNG
EVMIVDEFTGRVMDGRRYTDGLHQAIEAKEGVEIKNESKTMATVTYQNFF
RLYEKLSGMTGTAKTEEGEFESIYKLNVVQIPTNRPVIRADLHDKVFKTE
EEKYSAVVEEIIRIHKTRQPILVGTVSVEKSEKLSKMLKKQGIKHQVLNA
KQHDKEAEIISKAGKLDAITIATNMAGRGTDISLGAGDKEEEQEVKDLGG
LYVIGTERHESRRIDNQLRGRSGRQGDPGTSRFFVSLEDDVIKLYGGKTI
EKLMKRTSSNENTAIESKALTRAIERAQKGVEGKNFEIRKNVLKYDDTIN
EQRKVIYNERNKVLNDEDIQEDIQKMVKDIIQEAGETYLIGRKRDYYGYF
KHLYSTFMPADTLLIPGVDKKSVQEIIDSTYEISKRVYDLKKMMLGIDKV
AELEKTVLLKVVDQYWIDHIDAMEQLKQYIGLKSYAQKDPFKEYALEGYD
MFEALNKNIREATVQYLYKFN
Ligand information
Ligand IDAGS
InChIInChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
InChIKeyNLTUCYMLOPLUHL-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
ACDLabs 12.01O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC10 H16 N5 O12 P3 S
NamePHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
ATP-GAMMA-S;
ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
ChEMBLCHEMBL131890
DrugBankDB02930
ZINCZINC000008295128
PDB chain6t4h 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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PDB6t4h The Structure of Clostridioides difficile SecA2 ATPase Exposes Regions Responsible for Differential Target Recognition of the SecA1 and SecA2-Dependent Systems.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		M69 Y72 Q75 G93 G95 K96 T97 D197 G479
Binding residue
(residue number reindexed from 1)		M69 Y72 Q75 G93 G95 K96 T97 D197 G479
Annotation score1
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:0005829 cytosol
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:6t4h, PDBe:6t4h, PDBj:6t4h
PDBsum6t4h
PubMed32858965
UniProtQ183M9|SECA2_CLOD6 Protein translocase subunit SecA 2 (Gene Name=secA2)

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