Structure of PDB 4gil Chain A Binding Site BS01

Receptor Information
>4gil Chain A (length=307) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KISPELLQISPEVQDALKNKKPVVALESTIISHGMPFPQNAQTAIEVEET
IRKQGAVPATIAIIGGVMKVGLSKEEIELLGREGHNVTKVSRRDLPFVVA
AGKNGATTVASTMIIAALAGIKVFATGGIGGVHRGAEHTFDISADLQELA
NTNVTVVCAGAKSILDLGLTTEYLETFGVPLIGYQTKALPAFFCRTSPFD
VSIRLDSASEIARAMVVKWQSGLNGGLVVANPIPEQFAMPEHTINAAIDQ
AVAEAEAQGVIGKESTPFLLARVAELTGGDSLKSNIQLVFNNAILASEIA
KEYQRLA
Ligand information
Ligand IDKPS
InChIInChI=1S/C9H15N2O9P/c12-5(1-4-2-10-9(16)11-8(4)15)7(14)6(13)3-20-21(17,18)19/h2,5-7,12-14H,1,3H2,(H2,17,18,19)(H2,10,11,15,16)/t5-,6+,7-/m0/s1
InChIKeyGIMVKTFECLUQAU-XVMARJQXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C1=C(C(=O)NC(=O)N1)CC(C(C(COP(=O)(O)O)O)O)O
CACTVS 3.370O[CH](CO[P](O)(O)=O)[CH](O)[CH](O)CC1=CNC(=O)NC1=O
ACDLabs 12.01O=C1C(=CNC(=O)N1)CC(O)C(O)C(O)COP(=O)(O)O
OpenEye OEToolkits 1.7.6C1=C(C(=O)NC(=O)N1)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
CACTVS 3.370O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H](O)CC1=CNC(=O)NC1=O
FormulaC9 H15 N2 O9 P
Namepseudouridine 5'-phosphate, linear;
1-deoxy-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-ribitol
ChEMBL
DrugBank
ZINCZINC000098209085
PDB chain4gil Chain A 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]
PDB4gil Pseudouridine monophosphate glycosidase: a new glycosidase mechanism.
Resolution2.539 Å
Binding residue
(original residue number in PDB)
E31 T33 I34 K93 T112 V113 G131 G132 S147 D149 K166 N289
Binding residue
(residue number reindexed from 1)
E27 T29 I30 K89 T108 V109 G127 G128 S143 D145 K162 N285
Annotation score1
Enzymatic activity
Enzyme Commision number 4.2.1.70: pseudouridylate synthase.
Gene Ontology
Molecular Function
GO:0004730 pseudouridylate synthase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0016829 lyase activity
GO:0030145 manganese ion binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0001522 pseudouridine synthesis
GO:0046113 nucleobase catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0032991 protein-containing complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:4gil, PDBe:4gil, PDBj:4gil
PDBsum4gil
PubMed23066817
UniProtP33025|PSUG_ECOLI Pseudouridine-5'-phosphate glycosidase (Gene Name=psuG)

[Back to BioLiP]