Structure of PDB 7oyh Chain A Binding Site BS04

Receptor Information
>7oyh Chain A (length=471) Species: 28049 (Acidothermus cellulolyticus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MHRVMGIETEYGISVPHQPNANAMAASSQVVNAYAARWDFEGLANVILTN
GARLYVDHAHPEYSTPEVTNPRDAVLWDKAGERIMAEAARRAADLPMGWT
IQLYKNNTDNKGASYGCHENYLMNRSTPFADIVRHLIPFFVTRQVFCGAG
RVGIGADGRGEGFQLSQRADFFEVEVGLETTLKRPIINTRDEPHADPEKY
RRLHVIIGDANMSEIATYLKLGTTALVLAMIEDGFLSQDFSVESPVGALR
AVSHDPTLRYQLRLHDGRRLTAVQLQMEYLEQARKYVEDRFGTDVDDMTR
DVLDRWETTLVRLADDPMQLSRDLDWVAKLSILEGYRQRENLPWSAHKLQ
LVDLQYHDVRPDRGLYNRLVARGRMNLLVDEAAVRTAMHEPPNDTRAYFR
GRCLAKFGAEIAAASWDSVIFDLPGRDSLQRVPTLEPLRGTRAHVGDLLD
RCRSATELVAALTGGENLYFQ
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 chain7oyh Chain A Residue 605 [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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PDB7oyh Structures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		G6 E8 R90 Y92 S101 T102 E104 N157 L159 P230 W453
Binding residue
(residue number reindexed from 1)		G6 E8 R53 Y55 S64 T65 E67 N120 L122 P193 W416
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:7oyh, PDBe:7oyh, PDBj:7oyh
PDBsum7oyh
PubMed34789727
UniProtA0LU48|DOP_ACIC1 Depupylase (Gene Name=dop)

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