Structure of PDB 7oyf Chain A Binding Site BS05

Receptor Information
>7oyf Chain A (length=473) Species: 28049 (Acidothermus cellulolyticus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MHRVMGIETEYGISVPHQPNANAMAASSQVVNAYAQARWDFELGLANVIL
TNGARLYVDHAHPEYSTPEVTNPRDAVLWDKAGERIMAEAARRAADLPMG
WTIQLYKNNTDNKGASYGCHENYLMNRSTPFADIVRHLIPFFVTRQVFCG
AGRVGIGADGRGEGFQLSQRADFFEVEVGLETTLKRPIINTRDEPHADPE
KYRRLHVIIGDANMSEIATYLKLGTTALVLAMIEDGFLSQDFSVESPVGA
LRAVSHDPTLRYQLRLHDGRRLTAVQLQMEYLEQARKYVEDRFGTDVDDM
TRDVLDRWETTLVRLADDPMQLSRDLDWVAKLSILEGYRQRENLPWSAHK
LQLVDLQYHDVRPDRGLYNRLVARGRMNLLVDEAAVRTAMHEPPNDTRAY
FRGRCLAKFGAEIAAASWDSVIFDLPGRDSLQRVPTLEPLRGTRAHVGDL
LDRCRSATELVAALTGGENLYFQ
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 chain7oyf Chain A Residue 604 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7oyf Structures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation.
Resolution1.88 Å
Binding residue
(original residue number in PDB)		G6 E8 R90 Y92 S101 T102 E104 N157 L159 P230 R239 W453
Binding residue
(residue number reindexed from 1)		G6 E8 R55 Y57 S66 T67 E69 N122 L124 P195 R204 W418
Annotation score4
Enzymatic activity
Enzyme Commision number 3.4.-.-
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0008233 peptidase activity
GO:0016787 hydrolase activity
GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
GO:0046872 metal ion binding
Biological Process
GO:0010498 proteasomal protein catabolic process
GO:0019941 modification-dependent protein catabolic process
GO:0070490 protein pupylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7oyf, PDBe:7oyf, PDBj:7oyf
PDBsum7oyf
PubMed34789727
UniProtA0LU48|DOP_ACIC1 Depupylase (Gene Name=dop)

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