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BioLiP

Structure of PDB 7oxy Chain A Binding Site BS05

Receptor Information
>7oxy 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 IDACP
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
InChIKeyUFZTZBNSLXELAL-IOSLPCCCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
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)(CP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC11 H18 N5 O12 P3
NamePHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER;
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
ChEMBLCHEMBL133463
DrugBankDB03909
ZINCZINC000008295124
PDB chain7oxy Chain A Residue 610 [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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PDB7oxy Structures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		V4 G6 E8 R90 Y92 S101 T102 P103 E104 N157 L159 P230 R239 H241 W453
Binding residue
(residue number reindexed from 1)		V4 G6 E8 R55 Y57 S66 T67 P68 E69 N122 L124 P195 R204 H206 W418
Annotation score1
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:7oxy, PDBe:7oxy, PDBj:7oxy
PDBsum7oxy
PubMed34789727
UniProtA0LU48|DOP_ACIC1 Depupylase (Gene Name=dop)

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