Structure of PDB 6pod Chain B Binding Site BS02

Receptor Information
>6pod Chain B (length=350) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALPTPHEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGK
SNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGEDVENII
QKLLQKSDYDVQKAQRGIVYIDQIDKISRKSDNPSIDVSGEGVQQALLKL
IEGTVAAVPPQGGRKHPQQEFLQVDTSKILFICGGAFAGLDKVISHRVET
GSGIGFGATVKAKSDKASEGELLAQVEPEDLIKFGLIPEFIGRLPVVATL
NELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMA
RKTGARGLRSIVEAALLDTMYDLPSMEDVEKVVIDESVIDGQSEPLLIYG
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 chain6pod Chain B Residue 600 [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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PDB6pod Structures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate.
Resolution4.05 Å
Binding residue
(original residue number in PDB)		I79 G122 S123 G124 K125 T126 L127 I325 A369 R370
Binding residue
(residue number reindexed from 1)		I17 G60 S61 G62 K63 T64 L65 I261 A305 R306
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity
GO:0051082 unfolded protein binding
GO:0140662 ATP-dependent protein folding chaperone
Biological Process
GO:0006457 protein folding

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6pod, PDBe:6pod, PDBj:6pod
PDBsum6pod
PubMed32108573
UniProtP0A6H1|CLPX_ECOLI ATP-dependent Clp protease ATP-binding subunit ClpX (Gene Name=clpX)

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