Structure of PDB 5yfs Chain A Binding Site BS01

Receptor Information
>5yfs Chain A (length=322) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AMIVKEVYETAEKIKSMEIRGAGRIARAAAQALMIQAEKSKAKEPEELWN
ELKVASKILYNTRPTAVSLPNALRYVMHRVKAAYLGGADLETLRFTAINS
AKEFIYNSEKAIERIGEIGAKRIEDGDIIMTHSHSKAAISVMKKAFEQGK
NIKVIVTETRPKWQGKITAKELASYGIPVIYIVDSAARHYMKMTDKVVMG
ADSITANGAVINKIGTSLIALTAKEHRVWVMIAAETYKFHPATMLGQLVE
IEMRDPTEVIPEEELRTWPKNIEVWNPAFDVTPPEYIDVIITERGIIPPY
AAIDILKEEFGWALKYKEPWED
Ligand information
Ligand IDRI2
InChIInChI=1S/C5H12O11P2/c6-3-2(1-14-17(8,9)10)15-5(4(3)7)16-18(11,12)13/h2-7H,1H2,(H2,8,9,10)(H2,11,12,13)/t2-,3-,4-,5-/m1/s1
InChIKeyAAAFZMYJJHWUPN-TXICZTDVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C([C@@H]1[C@H]([C@H]([C@H](O1)OP(=O)(O)O)O)O)OP(=O)(O)O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)O[P](O)(O)=O
ACDLabs 12.01O=P(O)(O)OCC1OC(OP(=O)(O)O)C(O)C1O
OpenEye OEToolkits 1.7.0C(C1C(C(C(O1)OP(=O)(O)O)O)O)OP(=O)(O)O
CACTVS 3.370O[C@H]1[C@@H](O)[C@H](O[C@@H]1CO[P](O)(O)=O)O[P](O)(O)=O
FormulaC5 H12 O11 P2
Name1,5-di-O-phosphono-alpha-D-ribofuranose;
1,5-di-O-phosphono-alpha-D-ribose;
1,5-di-O-phosphono-D-ribose;
1,5-di-O-phosphono-ribose
ChEMBL
DrugBank
ZINCZINC000013522068
PDB chain5yfs 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

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PDB5yfs A presumed homologue of the regulatory subunits of eIF2B functions as ribose-1,5-bisphosphate isomerase in Pyrococcus horikoshii OT3.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		M19 R22 G23 A24 R65 S137 K138 A139 D204 N214 K215 K240 F281
Binding residue
(residue number reindexed from 1)		M17 R20 G21 A22 R63 S135 K136 A137 D202 N212 K213 K238 F279
Annotation score5
Binding affinityMOAD: Kd=13.8uM
PDBbind-CN: -logKd/Ki=4.86,Kd=13.8uM
Enzymatic activity
Enzyme Commision number 5.3.1.29: ribose-1,5-bisphosphate isomerase.
Gene Ontology
Molecular Function
GO:0016853 isomerase activity
GO:0043917 ribose 1,5-bisphosphate isomerase activity
GO:0046523 S-methyl-5-thioribose-1-phosphate isomerase activity
Biological Process
GO:0019323 pentose catabolic process
GO:0019509 L-methionine salvage from methylthioadenosine
GO:0044237 cellular metabolic process
GO:0044249 cellular biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5yfs, PDBe:5yfs, PDBj:5yfs
PDBsum5yfs
PubMed29382938
UniProtO57947|R15PI_PYRHO Ribose 1,5-bisphosphate isomerase (Gene Name=PH0208)

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