Structure of PDB 7qys Chain A Binding Site BS01

Receptor Information
>7qys Chain A (length=290) Species: 223283 (Pseudomonas syringae pv. tomato str. DC3000) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKIAVLSRNPRLYSTRRLVEAGIERGHEMVVIDTLRAYMNIASHKPQIHY
RGKPLEGFDAVIPRIGASVTFYGCAVLRQFEMMGVFPLNESVAIARSRDK
LRSLQLLSRRGIGLPVTGFAHSPDDIPDLIQMVNGAPLVIKVLEGTQGIG
VVLCETATAAESVIEAFMGLKQDIMVQEYIKEAGGADIRCFVVGDKVIAS
MKRQAKPGEFRSNLHRGGSASLIKITPEERMTALRAAKVMGLSVAGVDIL
RSNHGPLVMEVNSSPGLEGIEVTTSKDVAGMIIEYLEKNS
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 chain7qys Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7qys Structural insights into the mechanism of adaptive ribosomal modification by Pseudomonas RimK.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		V139 E178 Y179 I180 S212 L250 M259 E260
Binding residue
(residue number reindexed from 1)		V139 E178 Y179 I180 S212 L250 M259 E260
Annotation score4
Enzymatic activity
Enzyme Commision number 6.3.2.-
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0016881 acid-amino acid ligase activity
GO:0018169 ribosomal S6-glutamic acid ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0009432 SOS response
GO:0018410 C-terminal protein amino acid modification
GO:0036211 protein modification process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7qys, PDBe:7qys, PDBj:7qys
PDBsum7qys
PubMed36134899
UniProtQ88AZ9|RIMK_PSESM Probable alpha-L-glutamate ligase (Gene Name=rimK)

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