Structure of PDB 3gnd Chain K Binding Site BS01

Receptor Information
>3gnd Chain K (length=276) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GKDFRTDQPQKNIPFTLKGCGALDWGMQSRLSRIFNPKTGKTVMLAFDHG
YFQGPTTGLERIDINIAPLFEHADVLMCTRGILRSVVPPATNRPVVLRAS
GANSILAELSNEAVALSMDDAVRLNSCAVAAQVYIGSEYEHQSIKNIIQL
VDAGMKVGMPTMAVTGVVRDQRYFSLATRIAAEMGAQIIKTYYVEKGFER
IVAGCPVPIVIAGGKKLPEREALEMCWQAIDQGASGVDMGRNIFQSDHPV
AMMKAVQAVVHHNETADRAYELYLSE
Ligand information
Ligand ID5RP
InChIInChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/t4-,5+/m1/s1
InChIKeyFNZLKVNUWIIPSJ-UHNVWZDZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OCC(=O)[C@H](O)[C@H](O)CO[P](O)(O)=O
OpenEye OEToolkits 1.5.0C(C(C(C(=O)CO)O)O)OP(=O)(O)O
CACTVS 3.341OCC(=O)[CH](O)[CH](O)CO[P](O)(O)=O
ACDLabs 10.04O=P(O)(O)OCC(O)C(O)C(=O)CO
OpenEye OEToolkits 1.5.0C([C@H]([C@H](C(=O)CO)O)O)OP(=O)(O)O
FormulaC5 H11 O8 P
NameRIBULOSE-5-PHOSPHATE
ChEMBL
DrugBank
ZINCZINC000001532567
PDB chain3gnd Chain K Residue 984 [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]
PDB3gnd The crystal structure of the Escherichia coli autoinducer-2 processing protein LsrF.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		D57 H58 Y60 K203 G226 G227 D251 M252 G253 R254
Binding residue
(residue number reindexed from 1)		D48 H49 Y51 K190 G213 G214 D238 M239 G240 R241
Annotation score2
Enzymatic activity
Enzyme Commision number 2.3.1.245: 3-hydroxy-5-phosphooxypentane-2,4-dione thiolase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004332 fructose-bisphosphate aldolase activity
GO:0016740 transferase activity
GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups
GO:0016829 lyase activity
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:3gnd, PDBe:3gnd, PDBj:3gnd
PDBsum3gnd
PubMed19714241
UniProtP76143|LSRF_ECOLI 3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase (Gene Name=lsrF)

[Back to BioLiP]