Structure of PDB 5apg Chain B Binding Site BS01

Receptor Information
>5apg Chain B (length=184) Species: 572478 (Vulcanisaeta distributa DSM 14429) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIPRVFIYRLPQDDPRKNTAIKLVRFGFAQLVDSIKALPSGSIILDPTVK
TPLTPSDRVIAESRGLSLIDCSWKRAVDVHTKFIRGKFIRRRLPLLIAAN
PTHYGKPYILSTIEAVAAALYIMGFKDEAMEVLRLYKWGPNFIIINQKYL
ERYAAGDLSPERELLGVDDVDNGLEQLMRVLTNG
Ligand information
Ligand IDEEM
InChIInChI=1S/C15H22N6O5Se/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/p+1/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyGGJFWMOVUFBSIN-FCKMPRQPSA-O
SMILES
SoftwareSMILES
CACTVS 3.341C[Se+](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.341C[Se@@+](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[Se+](CCC(C(=O)O)N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
OpenEye OEToolkits 1.5.0C[Se@@+](CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04O=C(O)C(N)CC[Se+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H23 N6 O5 Se
Name[(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium;
Se-ADENOSYLSELENOMETHIONINE
ChEMBL
DrugBank
ZINC
PDB chain5apg Chain B Residue 1185 [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]
PDB5apg Ribosome Biogenesis Factor Tsr3 is the Aminocarboxypropyl Transferase Responsible for 18S Rrna Hypermodification in Yeast and Humans
Resolution1.6 Å
Binding residue
(original residue number in PDB)
N18 T19 P47 I69 C71 W73 L93 Y108 L110 S111 T112 A115
Binding residue
(residue number reindexed from 1)
N18 T19 P47 I69 C71 W73 L93 Y108 L110 S111 T112 A115
Annotation score3
Enzymatic activity
Enzyme Commision number 2.5.1.157: rRNA small subunit aminocarboxypropyltransferase.
Gene Ontology
Molecular Function
GO:0016740 transferase activity
GO:0106388 18S rRNA aminocarboxypropyltransferase activity
GO:1904047 S-adenosyl-L-methionine binding
Biological Process
GO:0000455 enzyme-directed rRNA pseudouridine synthesis
GO:0006364 rRNA processing
GO:0042254 ribosome biogenesis
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:5apg, PDBe:5apg, PDBj:5apg
PDBsum5apg
PubMed27084949
UniProtE1QU22|TSR3_VULDI 16S rRNA aminocarboxypropyltransferase (Gene Name=Vdis_0418)

[Back to BioLiP]