Structure of PDB 7qyr Chain E Binding Site BS02

Receptor Information
>7qyr Chain E (length=290) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKIAVLSRNPRLYSTRRLVEAGRERGHEMVVIDTLRAYMNIASHKPQIHY
RGQPLEGFDAVIPRIGASVTFYGCAVLRQFEMMGVFPLNESVAIARSRDK
LRSLQLLSRKGIGLPVTGFAHSPDDVPDLIEMVGGAPLVIKLLEGTQGIG
VVLCETEKAAESVLEAFMGLKHNIMVQEYIKEAGGADIRCFVVGDKVIAS
MKRQAAPGEFRSNLHRGGSASLIKITPEERMTAIRAARVMGLNVAGVDIL
RSNHGPLVMEVNSSPGLEGIESTTGKDIAGIIIQYLEKNG
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 chain7qyr Chain E Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7qyr Structural insights into the mechanism of adaptive ribosomal modification by Pseudomonas RimK.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		K141 Y179 F210 S212 L250 M259
Binding residue
(residue number reindexed from 1)		K141 Y179 F210 S212 L250 M259
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:0036211 protein modification process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7qyr, PDBe:7qyr, PDBj:7qyr
PDBsum7qyr
PubMed36134899
UniProtQ9HTZ2|RIMK_PSEAE Probable alpha-L-glutamate ligase (Gene Name=rimK)

[Back to BioLiP]