Structure of PDB 7sxo Chain D Binding Site BS01

Receptor Information
>7sxo Chain D (length=547) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TYKERIKSLKLPDSVQKIFDDEITKLSTLETSMSEFGVIRNYLDWLTSIP
WGKHSKEQYSIPRAKKILDEDHYGMVDVKDRILEFIAVGKLLGKVDGKII
CFVGPPGVGKTSIGKSIARALNRKFFRFSVGGMTDVAEIKGHRRTYIGAL
PGRVVQALKKCQTQNPLILIDEIDKIGHGGIHGDPSAALLEVLDPEQNNS
FLDNYLDIPIDLSKVLFVCTANSLETIPRPLLDRMEVIELTGYVAEDKVK
IAEQYLVPSAKKSAGLENSHVDMTEDAITALMKYYCRESGVRNLKKHIEK
IYRKAALQVVKKLEKINVSISQKNLKDYVGPPVYTTDRLYETTPPGVVMG
LAWTNMGGCSLYVESVLEQPLHNCKHPTFERTGQLGDVMKESSRLAYSFA
KMYLAQKFPENRFFEKASIHLHCPEGATPKDGPSAGVTMATSFLSLALNK
SIDPTVAMTGELTLTGKVLRIGGLREKAVAAKRSGAKTIIFPKDNLNDWE
ELPDNVKEGLEPLAADWYNDIFQKLFKDVNTKEGNSVWKAEFEILDA
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain7sxo Chain D Residue 1200 [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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PDB7sxo Cryo-EM structure of hexameric yeast Lon protease (PIM1) highlights the importance of conserved structural elements.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		H600 Y601 P634 G635 V636 G637 K638 T639 S640 Y771 I779 Y783 V819 K823
Binding residue
(residue number reindexed from 1)		H72 Y73 P106 G107 V108 G109 K110 T111 S112 Y243 I251 Y255 V291 K295
Annotation score5
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:0016887 ATP hydrolysis activity
Biological Process
GO:0006508 proteolysis
GO:0006515 protein quality control for misfolded or incompletely synthesized proteins
GO:0030163 protein catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7sxo, PDBe:7sxo, PDBj:7sxo
PDBsum7sxo
PubMed35143841
UniProtP36775|LONM_YEAST Lon protease homolog, mitochondrial (Gene Name=PIM1)

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