Structure of PDB 4b0t Chain B Binding Site BS02

Receptor Information
>4b0t Chain B (length=472) Species: 1718 (Corynebacterium glutamicum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
STVESALTRRIMGIETEYGLTFVDLRPDEIARRMFRPIVEKYSSSNIFIP
NGSRLYLDVGSHPEYATAECDNLTQLINFEKAGDVIADRMAVDAEESLAK
EDIAGQVYLFKNNVDSVGNSYGCHENYLVGRSMPLKALGKRLMPFLITRQ
LICGAGRIHHPNPLDKGESFPLGYCISQRSDHVWEGVSSATTRSRPIINT
RDEPHADSHSYRRLHVIVGDANMAEPSIALKVGSTLLVLEMIEADFGLPS
LELANDIASIREISRDATGSTLLSLKDGTTMTALQIQQVVFEHASKWLEQ
RPEPEFSGTSNTEMARVLDLWGRMLKAIESGDFSEVDTEIDWVIKKKLID
RFIQRGNLGLDDPKLAQVDLTYHDIRPGRGLFSVLQSRGMIKRWTTDEAI
LAAVDTAPDTTRAHLRGRILKAADTLGVPVTVDWMRHKVNRPEPQSVELG
DPFSAVNSEVDQLIEYMTVHAE
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 chain4b0t Chain B Residue 1479 [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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PDB4b0t Structures of Pup Ligase Pafa and Depupylase Dop from the Prokaryotic Ubiquitin-Like Modification Pathway.
Resolution2.159 Å
Binding residue
(original residue number in PDB)		R60 T73 E75 N132 L134 P210 H211 R219 W440 P458
Binding residue
(residue number reindexed from 1)		R54 T67 E69 N126 L128 P204 H205 R213 W434 P452
Annotation score4
Enzymatic activity
Enzyme Commision number 6.3.1.19: prokaryotic ubiquitin-like protein ligase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0016879 ligase activity, forming carbon-nitrogen bonds
GO:0019787 ubiquitin-like protein transferase activity
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:4b0t, PDBe:4b0t, PDBj:4b0t
PDBsum4b0t
PubMed22910360
UniProtQ8NQE1|PAFA_CORGL Pup--protein ligase (Gene Name=pafA)

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