Structure of PDB 2nx3 Chain B Binding Site BS02

Receptor Information
>2nx3 Chain B (length=262) Species: 63363 (Aquifex aeolicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KFLVIAGPNAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSI
HSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPA
FLCRQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLT
ERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQLPGGLGDKSGGMRE
FIFPLIRAAVAVGCDGVFMETHPEPEKALSDAPTALPLSQLEGIIEAILE
IREVASKYYETI
Ligand information
Ligand IDA5P
InChIInChI=1S/C5H13O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h3-9H,1-2H2,(H2,10,11,12)/t3-,4-,5+/m1/s1
InChIKeyVJDOAZKNBQCAGE-WDCZJNDASA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[C@@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O
OpenEye OEToolkits 1.5.0C(C(C(C(COP(=O)(O)O)O)O)O)O
CACTVS 3.341OC[CH](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@@H](COP(=O)(O)O)O)O)O)O
FormulaC5 H13 O8 P
NameARABINOSE-5-PHOSPHATE
ChEMBL
DrugBankDB03745
ZINCZINC000003871578
PDB chain2nx3 Chain B Residue 269 [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]
PDB2nx3 Structural and Mechanistic Changes along an Engineered Path from Metallo to Nonmetallo 3-Deoxy-d-manno-octulosonate 8-Phosphate Synthases.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		N11 K46 N48 R49 S50 H185 Q188 K196 S197 D233
Binding residue
(residue number reindexed from 1)		N9 K44 N46 R47 S48 H183 Q186 K194 S195 D231
Annotation score2
Binding affinityMOAD: Kd=17uM
Enzymatic activity
Enzyme Commision number 2.5.1.55: 3-deoxy-8-phosphooctulonate synthase.
Gene Ontology
Molecular Function
GO:0008676 3-deoxy-8-phosphooctulonate synthase activity
GO:0016740 transferase activity
Biological Process
GO:0009058 biosynthetic process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0019294 keto-3-deoxy-D-manno-octulosonic acid biosynthetic process
GO:0046364 monosaccharide biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2nx3, PDBe:2nx3, PDBj:2nx3
PDBsum2nx3
PubMed17381075
UniProtO66496|KDSA_AQUAE 2-dehydro-3-deoxyphosphooctonate aldolase (Gene Name=kdsA)

[Back to BioLiP]