Structure of PDB 4b0t Chain B Binding Site BS01

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 A Residue 1478 [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)		I12 E16 P450
Binding residue
(residue number reindexed from 1)		I11 E15 P444
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

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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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