Structure of PDB 7yph Chain D Binding Site BS01

Receptor Information
>7yph Chain D (length=773) Species: 172827 (Meiothermus taiwanensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RLELPVIPLRNTVILPHTTTPVDVGRAKSKRAVEEAMGADRLIFLVAQRD
PEVDDPAPDDLYTWGVQAVVKQAMRLPDGTLQVMVEARARAQVTDYIPGP
YLRARGEVFSEIFPIDEAVVRVLVEELKEAFEKYVANHKSLRLDRYQLEA
VKGTSDPAMLADTIAYHATWTVAEKQEILELTDLEARLKKVLGLLSRDLE
RFELDKRVAQRVKEQMDTNQRESYLREQMKAIQKELGGEDGLSDLEALRK
KIEEVGMPEAVKTKALKELDRLERMQQGSPEATVARTYLDWLTEVPWSKA
DPEVLDINHTRQVLDEDHYGLKDVKERILEYLAVRQLTQGLDVRNKAPIL
VLVGPPGVGKTSLGRSIARSMNRKFHRISLGGVRDEAEIRGHRRTYIGAM
PGKLIHAMKQVGVINPVILLDEIDKMSSDWRGDPASAMLEVLDPEQNNTF
TDHYLDVPYDLSKVFFITTANTLQTIPRPLLDRMEVIEIPGYTNMEKQAI
ARQYLWPKQVRESGMEGRIEVTDAAILRVISEYTREAGVRGLERELGKIA
RKGAKFWLEGAWEGLRTIDASDIPTYLGIPRYRPDKAETEPQVGTAQGLA
WTPVGGTLLTIEVAAVPGSGKLSLTGQLGEVMKESAQAALTYLRAHTQDY
GLPEDFYNKVDLHVHVPDGATPKDGPSAGITMATAIASALSRRPARMDIA
MTGEVSLRGKVMPIGGVKEKLLAAHQAGIHKIVLPKDNEAQLEELPKEVL
EGLEIKLVEDVGEVLEYLLLPEP
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 chain7yph Chain D 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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PDB7yph A 5+1 assemble-to-activate mechanism of the Lon proteolytic machine
Resolution3.68 Å
Binding residue
(original residue number in PDB)		H319 P357 G358 V359 G360 K361 T362 S363 R366 R378 D422 Y493 I501 K509 V540 R541
Binding residue
(residue number reindexed from 1)		H318 P356 G357 V358 G359 K360 T361 S362 R365 R377 D421 Y492 I500 K508 V539 R540
Annotation score4
Enzymatic activity
Enzyme Commision number 3.4.21.53: endopeptidase La.
Gene Ontology
Molecular Function
GO:0004176 ATP-dependent peptidase activity
GO:0004252 serine-type endopeptidase activity
GO:0005524 ATP binding
GO:0008236 serine-type peptidase activity
GO:0016887 ATP hydrolysis activity
GO:0042802 identical protein binding
GO:0043565 sequence-specific DNA binding
GO:0046872 metal ion binding
Biological Process
GO:0006508 proteolysis
GO:0006515 protein quality control for misfolded or incompletely synthesized proteins
GO:0030163 protein catabolic process
GO:0034605 cellular response to heat
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7yph, PDBe:7yph, PDBj:7yph
PDBsum7yph
PubMed37957149
UniProtA0A059VAZ3

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