Structure of PDB 8k06 Chain B Binding Site BS01

Receptor Information
>8k06 Chain B (length=304) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RSLVKISPQVSEALSNGRAVVALESTIISHGMPYPQNLQTAKEVESIVRE
NGAIPATIAILNGVPCIGLSEEELERLASLGKSVQKTAGRDIANVVATRG
NGATTVSATLFFASMVGIQVFVTGGIGGVHRHANHSMDISSDLTALGRTP
IAVISAGVASILDIPKTLEYLETQEVYVAAYKSDEFPAFFTEKSGCKAPS
RVNSPEDCARVIDANMKLNRQAGILFAIPIPKHHSAAGNLIESATQRALT
EAREQNVTGNAETPFLLARVNELTGGTSLAANIALVKNNALIGSQIAVAL
SQLM
Ligand information
Ligand IDRP5
InChIInChI=1S/C5H11O8P/c6-3-2(1-12-14(9,10)11)13-5(8)4(3)7/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1
InChIKeyKTVPXOYAKDPRHY-TXICZTDVSA-N
SMILES
SoftwareSMILES
CACTVS 3.370O[CH]1O[CH](CO[P](O)(O)=O)[CH](O)[CH]1O
OpenEye OEToolkits 1.7.0C([C@@H]1[C@H]([C@H]([C@@H](O1)O)O)O)OP(=O)(O)O
OpenEye OEToolkits 1.7.0C(C1C(C(C(O1)O)O)O)OP(=O)(O)O
CACTVS 3.370O[C@@H]1O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]1O
ACDLabs 12.01O=P(O)(O)OCC1OC(O)C(O)C1O
FormulaC5 H11 O8 P
Name5-O-phosphono-beta-D-ribofuranose;
[(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE;
5-O-phosphono-beta-D-ribose;
5-O-phosphono-D-ribose;
5-O-phosphono-ribose
ChEMBLCHEMBL1235722
DrugBankDB04352
ZINCZINC000004228241
PDB chain8k06 Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8k06 Structure and function of the pseudouridine 5'-monophosphate glycosylase PUMY from Arabidopsis thaliana.
Resolution1.845 Å
Binding residue
(original residue number in PDB)
K112 R116 T131 S166 S167
Binding residue
(residue number reindexed from 1)
K86 R90 T105 S140 S141
Annotation score5
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:0030597 RNA glycosylase activity
GO:0046872 metal ion binding
Biological Process
GO:0001522 pseudouridine synthesis
Cellular Component
GO:0005777 peroxisome

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:8k06, PDBe:8k06, PDBj:8k06
PDBsum8k06
PubMed38117089
UniProtQ84K35|PUMY_ARATH Pseudouridine-5'-phosphate glycosidase (Gene Name=PUMY)

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